| Order | Family | Species | Occurrence | FishBase name | Name in Country |
|---|---|---|---|---|---|
| Tetraodontiformes | Balistidae | Abalistes filamentosus | native | ||
| Tetraodontiformes | Balistidae | Abalistes stellatus | native | Starry triggerfish | |
| Lophiiformes | Antennariidae | Abantennarius coccineus | native | Scarlet frogfish | |
| Lophiiformes | Antennariidae | Abantennarius dorehensis | native | New Guinean frogfish | |
| Lophiiformes | Antennariidae | Abantennarius nummifer | native | Spotfin frogfish | |
| Lophiiformes | Antennariidae | Abantennarius rosaceus | native | Spiny-tufted frogfish | |
| Ovalentaria/misc | Pomacentridae | Abudefduf bengalensis | native | Bengal sergeant | |
| Ovalentaria/misc | Pomacentridae | Abudefduf notatus | native | Yellowtail sergeant | |
| Ovalentaria/misc | Pomacentridae | Abudefduf septemfasciatus | native | Banded sergeant | |
| Ovalentaria/misc | Pomacentridae | Abudefduf sexfasciatus | native | Scissortail sergeant | |
| Ovalentaria/misc | Pomacentridae | Abudefduf sordidus | native | Blackspot sergeant | |
| Ovalentaria/misc | Pomacentridae | Abudefduf vaigiensis | native | Indo-Pacific sergeant | |
| Scombriformes | Scombridae | Acanthocybium solandri | native | Wahoo | |
| Gobiiformes | Gobiidae | Acanthogobius insularis | native | ||
| Eupercaria/misc | Sparidae | Acanthopagrus chinshira | native | Okinawan yellow-fin seabream | |
| Eupercaria/misc | Sparidae | Acanthopagrus pacificus | native | Pacific seabream | |
| Eupercaria/misc | Sparidae | Acanthopagrus sivicolus | endemic | Okinawa seabream | |
| Acanthuriformes | Acanthuridae | Acanthurus bariene | native | Black-spot surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus blochii | native | Ringtail surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus dussumieri | native | Eyestripe surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus guttatus | native | Whitespotted surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus japonicus | native | Japan surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus leucopareius | native | Whitebar surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus lineatus | native | Lined surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus maculiceps | native | White-freckled surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus mata | native | Elongate surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus nigricans | native | Whitecheek surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus nigricauda | native | Epaulette surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus nigrofuscus | native | Brown surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus olivaceus | native | Orangespot surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus pyroferus | native | Chocolate surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus thompsoni | native | Thompson's surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus triostegus | native | Convict surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus xanthopterus | native | Yellowfin surgeonfish | |
| Gobiiformes | Gobiidae | Acentrogobius audax | native | Mangrove goby | |
| Gobiiformes | Gobiidae | Acentrogobius janthinopterus | native | Robust mangrove goby | |
| Gobiiformes | Gobiidae | Acentrogobius moloanus | native | Barcheek Amoya | |
| Gobiiformes | Gobiidae | Acentrogobius multifasciatus | native | ||
| Gobiiformes | Gobiidae | Acentrogobius nebulosus | native | Shadow goby | |
| Gobiiformes | Gobiidae | Acentrogobius pflaumii | native | Striped sandgoby | |
| Gobiiformes | Gobiidae | Acentrogobius suluensis | native | Sulu goby | |
| Gobiiformes | Gobiidae | Acentrogobius viganensis | native | ||
| Gobiiformes | Gobiidae | Acentrogobius viridipunctatus | native | Spotted green goby | |
| Tetraodontiformes | Monacanthidae | Acreichthys hajam | native | ||
| Tetraodontiformes | Monacanthidae | Acreichthys radiatus | native | Radial leatherjacket | |
| Tetraodontiformes | Monacanthidae | Acreichthys tomentosus | native | Bristle-tail file-fish | |
| Perciformes/Serranoidei | Epinephelidae | Aethaloperca rogaa | native | Redmouth grouper | |
| Myliobatiformes | Myliobatidae | Aetomylaeus nichofii | native | Banded eagle ray | |
| Carangiformes | Carangidae | Alectis ciliaris | native | African pompano | |
| Carangiformes | Carangidae | Alepes djedaba | native | Shrimp scad | |
| Carangiformes | Carangidae | Alepes kleinii | native | Razorbelly scad | |
| Carangiformes | Carangidae | Alepes melanoptera | native | Blackfin scad | |
| Carangiformes | Carangidae | Alepes vari | native | Herring scad | |
| Alepocephaliformes | Alepocephalidae | Alepocephalus bicolor | native | Bicolor slickhead | |
| Alepocephaliformes | Alepocephalidae | Alepocephalus longiceps | native | Longfin slickhead | |
| Alepocephaliformes | Alepocephalidae | Alepocephalus longirostris | native | Longsnout slickhead | |
| Alepocephaliformes | Alepocephalidae | Alepocephalus owstoni | native | Owston's slickhead | |
| Alepocephaliformes | Alepocephalidae | Alepocephalus triangularis | native | Triangulate slickhead | |
| Ophidiiformes | Dinematichthyidae | Alionematichthys riukiuensis | native | Bigeye cusk | |
| Ophidiiformes | Dinematichthyidae | Alionematichthys shinoharai | native | ||
| Lamniformes | Alopiidae | Alopias pelagicus | native | Pelagic thresher | |
| Blenniiformes | Blenniidae | Alticus saliens | native | Leaping blenny | |
| Eupercaria/misc | Sparidae | Amamiichthys matsubarai | native | Japanese blue-spotted seabream | |
| Ovalentaria/misc | Ambassidae | Ambassis buruensis | native | Buru glass perchlet | |
| Ovalentaria/misc | Ambassidae | Ambassis interrupta | native | Long-spined glass perchlet | |
| Centrarchiformes | Cirrhitidae | Amblycirrhitus bimacula | native | Twospot hawkfish | |
| Centrarchiformes | Cirrhitidae | Amblycirrhitus unimacula | native | ||
| Gobiiformes | Gobiidae | Amblyeleotris diagonalis | native | Diagonal shrimp goby | |
| Gobiiformes | Gobiidae | Amblyeleotris fasciata | native | Red-banded prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris fontanesii | native | Giant prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris guttata | native | Spotted prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris japonica | native | ||
| Gobiiformes | Gobiidae | Amblyeleotris masuii | native | Masui's shrimp-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris melanocephala | native | Blackhead shrimpgoby | |
| Gobiiformes | Gobiidae | Amblyeleotris ogasawarensis | native | Redspotted shrimpgoby | |
| Gobiiformes | Gobiidae | Amblyeleotris periophthalma | native | Periophthalma prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris randalli | native | Randall's prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris wheeleri | native | Gorgeous prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris yanoi | native | Flagtail shrimpgoby | |
| Clupeiformes | Dorosomatidae | Amblygaster leiogaster | native | Smoothbelly sardinella | |
| Clupeiformes | Dorosomatidae | Amblygaster sirm | native | Spotted sardinella | |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon aureus | native | Golden damselfish | |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon curacao | native | Staghorn damselfish | |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon leucogaster | native | Yellowbelly damselfish | |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon ternatensis | native | Ternate damsel | |
| Gobiiformes | Gobiidae | Amblygobius decussatus | native | Orange-striped goby | |
| Gobiiformes | Gobiidae | Amblygobius nocturnus | native | Nocturn goby | |
| Gobiiformes | Gobiidae | Amblygobius phalaena | native | Whitebarred goby | |
| Ovalentaria/misc | Pomacentridae | Amblypomacentrus tricinctus | native | Threeband damselfish | |
| Kurtiformes | Apogonidae | Amioides polyacanthus | native | ||
| Ovalentaria/misc | Pomacentridae | Amphiprion clarkii | native | Yellowtail clownfish | |
| Ovalentaria/misc | Pomacentridae | Amphiprion frenatus | native | Tomato clownfish | |
| Ovalentaria/misc | Pomacentridae | Amphiprion ocellaris | native | Clown anemonefish | |
| Ovalentaria/misc | Pomacentridae | Amphiprion perideraion | native | Pink anemonefish | |
| Ovalentaria/misc | Pomacentridae | Amphiprion polymnus | native | Saddleback clownfish | |
| Ovalentaria/misc | Pomacentridae | Amphiprion sandaracinos | native | Yellow clownfish | |
| Eupercaria/misc | Labridae | Anampses caeruleopunctatus | native | Bluespotted wrasse | |
| Eupercaria/misc | Labridae | Anampses geographicus | native | Geographic wrasse | |
| Eupercaria/misc | Labridae | Anampses melanurus | native | White-spotted wrasse | |
| Eupercaria/misc | Labridae | Anampses meleagrides | native | Spotted wrasse | |
| Eupercaria/misc | Labridae | Anampses twistii | native | Yellowbreasted wrasse | |
| Callionymiformes | Callionymidae | Anaora tentaculata | native | Tentacled dragonet | |
| Gobiiformes | Gobiidae | Ancistrogobius dipus | native | Double-fin cheek-hook goby | |
| Gobiiformes | Gobiidae | Ancistrogobius squamiceps | native | Scaly cheek-hook goby | |
| Gobiiformes | Gobiidae | Ancistrogobius yanoi | native | Yano’s cheek-hook goby | |
| Gobiiformes | Gobiidae | Ancistrogobius yoshigoui | native | Threadless cheek-hook goby | |
| Blenniiformes | Blenniidae | Andamia tetradactylus | native | Four-fingered lipsucker | |
| Anguilliformes | Anguillidae | Anguilla marmorata | native | Giant mottled eel | |
| Trachichthyiformes | Anomalopidae | Anomalops katoptron | native | Splitfin flashlightfish | |
| Lophiiformes | Antennariidae | Antennarius maculatus | native | Warty frogfish | |
| Lophiiformes | Antennariidae | Antennatus tuberosus | native | Tuberculated frogfish | |
| Perciformes/Serranoidei | Epinephelidae | Anyperodon leucogrammicus | native | Slender grouper | |
| Eupercaria/misc | Lutjanidae | Aphareus furca | native | Small toothed jobfish | |
| Eupercaria/misc | Lutjanidae | Aphareus rutilans | native | Rusty jobfish | |
| Kurtiformes | Apogonidae | Apogon caudicinctus | native | Little tailband cardinalfish | |
| Kurtiformes | Apogonidae | Apogon crassiceps | native | Transparent cardinalfish | |
| Kurtiformes | Apogonidae | Apogon doryssa | native | Longspine cardinalfish | |
| Kurtiformes | Apogonidae | Apogon seminigracaudus | native | Darktail cardinalfish | |
| Kurtiformes | Apogonidae | Apogon semiornatus | native | Oblique-banded cardinalfish | |
| Kurtiformes | Apogonidae | Apogon talboti | native | Flame cardinalfish | |
| Kurtiformes | Apogonidae | Apogonichthyoides cathetogramma | native | ||
| Kurtiformes | Apogonidae | Apogonichthyoides melas | native | Black cardinalfish | |
| Acanthuriformes | Pomacanthidae | Apolemichthys trimaculatus | native | Threespot angelfish | |
| Perciformes/Serranoidei | Grammistidae | Aporops bilinearis | native | Blotched podge | |
| Eupercaria/misc | Lutjanidae | Aprion virescens | native | Green jobfish | |
| Carcharhiniformes | Pentanchidae | Apristurus japonicus | native | Japanese catshark | |
| Carcharhiniformes | Pentanchidae | Apristurus macrorhynchus | native | Flathead catshark | |
| Gobiiformes | Gobiidae | Arcygobius baliurus | native | Isthmus goby | |
| Eupercaria/misc | Sciaenidae | Argyrosomus japonicus | native | Japanese meagre | |
| Scombriformes | Ariommatidae | Ariomma brevimanus | native | ||
| Tetraodontiformes | Tetraodontidae | Arothron carduus | native | ||
| Tetraodontiformes | Tetraodontidae | Arothron immaculatus | native | Immaculate puffer | |
| Tetraodontiformes | Tetraodontidae | Arothron manilensis | native | Narrow-lined puffer | |
| Tetraodontiformes | Tetraodontidae | Arothron mappa | native | Map puffer | |
| Tetraodontiformes | Tetraodontidae | Arothron meleagris | native | Guineafowl puffer | |
| Tetraodontiformes | Tetraodontidae | Arothron nigropunctatus | native | Blackspotted puffer | |
| Tetraodontiformes | Tetraodontidae | Arothron reticularis | native | Reticulated pufferfish | |
| Ovalentaria/misc | Plesiopidae | Assessor randalli | native | ||
| Scombriformes | Trichiuridae | Assurger anzac | native | Razorback scabbardfish | |
| Pleuronectiformes | Bothidae | Asterorhombus cocosensis | native | Cocos Island flounder | |
| Gobiiformes | Gobiidae | Asterropteryx atripes | native | Yano’s starry goby | |
| Gobiiformes | Gobiidae | Asterropteryx ensifera | native | Miller's damsel | |
| Gobiiformes | Gobiidae | Asterropteryx ovata | native | Oval-spot goby | |
| Gobiiformes | Gobiidae | Asterropteryx semipunctata | native | Starry goby | |
| Gobiiformes | Gobiidae | Asterropteryx senoui | native | Senou's goby | |
| Gobiiformes | Gobiidae | Asterropteryx spinosa | native | Eyebar spiny goby | |
| Atheriniformes | Atherinidae | Atherinomorus lacunosus | native | Wide-banded hardyhead silverside | |
| Atheriniformes | Atherinidae | Atherinomorus pinguis | native | Narrow-banded hardyhead silverside | |
| Carangiformes | Carangidae | Atropus armatus | native | Longfin trevally | |
| Carangiformes | Carangidae | Atropus hedlandensis | native | Bumpnose trevally | |
| Carangiformes | Carangidae | Atropus mentalis | native | Longrakered trevally | |
| Blenniiformes | Blenniidae | Atrosalarias fuscus | native | ||
| Blenniiformes | Blenniidae | Atrosalarias holomelas | native | Brown coral blenny | |
| Blenniiformes | Blenniidae | Atrosalarias hosokawai | native | Hosokawa's coral blenny | |
| Carangiformes | Carangidae | Atule mate | native | Yellowtail scad | |
| Acanthuriformes | Leiognathidae | Aurigequula fasciata | native | Striped ponyfish | |
| Scombriformes | Scombridae | Auxis rochei | native | Bullet tuna | |
| Scombriformes | Scombridae | Auxis thazard | native | Frigate tuna | |
| Ovalentaria/misc | Pomacentridae | Azurina elerae | native | Twinspot chromis | |
| Ovalentaria/misc | Pomacentridae | Azurina lepidolepis | native | Scaly chromis | |
| Gobiiformes | Gobiidae | Barbuligobius boehlkei | native | Cryptic bearded goby | |
| Anguilliformes | Ophichthidae | Bascanichthys ryukyuensis | native | Vine-like sand eel | |
| Gobiiformes | Gobiidae | Bathygobius coalitus | native | Whitespotted frillgoby | |
| Gobiiformes | Gobiidae | Bathygobius fuscus | native | Dusky frillgoby | |
| Ovalentaria/misc | Plesiopidae | Belonepterygion fasciolatum | native | Barred spiny basslet | |
| Perciformes/Serranoidei | Liopropomatidae | Belonoperca chabanaudi | native | Arrowhead soapfish | |
| Scombriformes | Trichiuridae | Benthodesmus pacificus | native | North-Pacific frostfish | |
| Scombriformes | Trichiuridae | Benthodesmus tenuis | native | Slender frostfish | |
| Scombriformes | Trichiuridae | Benthodesmus vityazi | native | Vityaz' frostfish | |
| Beryciformes | Berycidae | Beryx mollis | native | ||
| Blenniiformes | Blenniidae | Blenniella bilitonensis | native | Biliton blenniella | |
| Blenniiformes | Blenniidae | Blenniella caudolineata | native | Blue-spotted blenny | |
| Blenniiformes | Blenniidae | Blenniella chrysospilos | native | Red-spotted blenny | |
| Blenniiformes | Blenniidae | Blenniella periophthalmus | native | Blue-dashed rockskipper | |
| Eupercaria/misc | Labridae | Bodianus bilunulatus | native | Tarry hogfish | |
| Eupercaria/misc | Labridae | Bodianus bimaculatus | native | Twospot hogfish | |
| Eupercaria/misc | Labridae | Bodianus loxozonus | native | Blackfin hogfish | |
| Eupercaria/misc | Labridae | Bodianus masudai | native | ||
| Eupercaria/misc | Labridae | Bodianus mesothorax | native | Splitlevel hogfish | |
| Eupercaria/misc | Labridae | Bodianus rubrisos | native | Red-sashed hogfish | |
| Eupercaria/misc | Labridae | Bodianus tanyokidus | native | ||
| Eupercaria/misc | Scaridae | Bolbometopon muricatum | native | Green humphead parrotfish | |
| Myctophiformes | Myctophidae | Bolinichthys distofax | native | ||
| Myctophiformes | Myctophidae | Bolinichthys longipes | native | Popeye lampfish | |
| Gobiiformes | Butidae | Bostrychus sinensis | native | Four-eyed sleeper | |
| Pleuronectiformes | Bothidae | Bothus mancus | native | Flowery flounder | |
| Pleuronectiformes | Soleidae | Brachirus orientalis | native | Oriental sole | |
| Anguilliformes | Ophichthidae | Brachysomophis crocodilinus | native | Crocodile snake eel | |
| Anguilliformes | Ophichthidae | Brachysomophis henshawi | native | Reptilian snake eel | |
| Scombriformes | Bramidae | Brama orcini | native | Bigtooth pomfret | |
| Eupercaria/misc | Latilidae | Branchiostegus japonicus | native | Horsehead tilefish | |
| Ophidiiformes | Bythitidae | Brosmophyciops pautzkei | native | Slimy cuskeel | |
| Gobiiformes | Gobiidae | Bryaninops amplus | native | Large whip goby | |
| Gobiiformes | Gobiidae | Bryaninops erythrops | native | Erythrops goby | |
| Gobiiformes | Gobiidae | Bryaninops isis | native | Isis goby | |
| Gobiiformes | Gobiidae | Bryaninops loki | native | Loki whip-goby | |
| Gobiiformes | Gobiidae | Bryaninops natans | native | Redeye goby | |
| Gobiiformes | Gobiidae | Bryaninops nexus | native | Upside-down goby | |
| Gobiiformes | Gobiidae | Bryaninops ridens | native | Ridens goby | |
| Gobiiformes | Gobiidae | Bryaninops tigris | native | Black coral goby | |
| Gobiiformes | Gobiidae | Bryaninops yongei | native | Whip coral goby | |
| Gobiiformes | Butidae | Butis amboinensis | native | Olive flathead-gudgeon | |
| Gobiiformes | Gobiidae | Cabillus lacertops | native | Lizard cabillus | |
| Gobiiformes | Gobiidae | Cabillus tongarevae | native | Tongareva goby | |
| Eupercaria/misc | Caesionidae | Caesio caerulaurea | native | Blue and gold fusilier | |
| Eupercaria/misc | Caesionidae | Caesio cuning | native | Redbelly yellowtail fusilier | |
| Eupercaria/misc | Caesionidae | Caesio lunaris | native | Lunar fusilier | |
| Eupercaria/misc | Caesionidae | Caesio teres | native | Yellow and blueback fusilier | |
| Anguilliformes | Ophichthidae | Callechelys catostoma | native | Black-striped snake eel | |
| Callionymiformes | Callionymidae | Callionymus enneactis | native | Mangrove dragonet | |
| Callionymiformes | Callionymidae | Callionymus ikedai | native | Ryukyu ruddertail dragonet | |
| Callionymiformes | Callionymidae | Callionymus japonicus | native | Japanese longtail dragonet | |
| Callionymiformes | Callionymidae | Callionymus ochiaii | native | Japanese lowfin deepwater dragonet | |
| Callionymiformes | Callionymidae | Callionymus pleurostictus | native | Blue-spotted ruddertail dragonet | |
| Gobiiformes | Gobiidae | Callogobius hasseltii | native | Hasselt's goby | |
| Gobiiformes | Gobiidae | Callogobius maculipinnis | native | Ostrich goby | |
| Gobiiformes | Gobiidae | Callogobius okinawae | native | Okinawa flap-headed goby | |
| Gobiiformes | Gobiidae | Callogobius sclateri | native | Pacific goby | |
| Gobiiformes | Gobiidae | Callogobius snelliusi | native | ||
| Gobiiformes | Gobiidae | Callogobius tanegasimae | native | ||
| Ovalentaria/misc | Plesiopidae | Calloplesiops altivelis | native | Comet | |
| Eupercaria/misc | Scaridae | Calotomus carolinus | native | Carolines parrotfish | |
| Eupercaria/misc | Scaridae | Calotomus spinidens | native | Spinytooth parrotfish | |
| Gobiiformes | Eleotridae | Calumia godeffroyi | native | Tailface sleeper | |
| Tetraodontiformes | Monacanthidae | Cantherhines fronticinctus | native | Spectacled filefish | |
| Tetraodontiformes | Tetraodontidae | Canthigaster axiologus | native | Pacific crown toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster compressa | native | Compressed toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster epilampra | native | Lantern toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster ocellicincta | native | Shy toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster solandri | native | Spotted sharpnose | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Caracanthus maculatus | native | Spotted coral croucher | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Caracanthus unipinna | native | Pygmy coral croucher | |
| Gobiiformes | Gobiidae | Caragobius urolepis | native | Scaleless worm goby | |
| Carangiformes | Carangidae | Carangichthys dinema | native | Shadow trevally | |
| Carangiformes | Carangidae | Carangichthys oblongus | native | Coachwhip trevally | |
| Carangiformes | Carangidae | Caranx heberi | native | Blacktip trevally | |
| Carangiformes | Carangidae | Caranx ignobilis | native | Giant trevally | |
| Carangiformes | Carangidae | Caranx melampygus | native | Bluefin trevally | |
| Carangiformes | Carangidae | Caranx papuensis | native | Brassy trevally | |
| Carangiformes | Carangidae | Caranx sexfasciatus | native | Bigeye trevally | |
| Carangiformes | Carangidae | Caranx tille | native | Tille trevally | |
| Ophidiiformes | Carapidae | Carapus mourlani | native | Star pearlfish | |
| Carcharhiniformes | Carcharhinidae | Carcharhinus melanopterus | native | Blacktip reef shark | |
| Carcharhiniformes | Carcharhinidae | Carcharhinus plumbeus | native | Sandbar shark | |
| Lamniformes | Lamnidae | Carcharodon carcharias | native | Great white shark | |
| Myctophiformes | Myctophidae | Centrobranchus andreae | native | Andre's lanternfish | |
| Myctophiformes | Myctophidae | Centrobranchus brevirostris | native | ||
| Myctophiformes | Myctophidae | Centrobranchus choerocephalus | native | ||
| Eupercaria/misc | Centrogenyidae | Centrogenys vaigiensis | native | False scorpionfish | |
| Squaliformes | Centrophoridae | Centrophorus granulosus | native | Gulper shark | |
| Squaliformes | Centrophoridae | Centrophorus moluccensis | native | Smallfin gulper shark | |
| Acanthuriformes | Pomacanthidae | Centropyge bicolor | native | Bicolor angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge bispinosa | native | Twospined angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge ferrugata | native | Rusty angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge fisheri | native | Orange angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge flavissima | native | Lemonpeel angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge heraldi | native | Yellow angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge nox | native | Midnight angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge tibicen | native | Keyhole angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge venusta | native | Purplemask angelfish | |
| Acanthuriformes | Pomacanthidae | Centropyge vrolikii | native | Pearlscale angelfish | |
| Squaliformes | Etmopteridae | Centroscyllium kamoharai | native | Bareskin dogfish | |
| Squaliformes | Somniosidae | Centroscymnus owstonii | native | Roughskin dogfish | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis argus | native | Peacock hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis aurantia | native | Golden hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis boenak | native | Chocolate hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis igarashiensis | native | Garish hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis leopardus | native | Leopard hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis miniata | native | Coral hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis polleni | native | Harlequin hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis sexmaculata | native | Sixblotch hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis sonnerati | native | Tomato hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis spiloparaea | native | Strawberry hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis urodeta | native | Darkfin hind | |
| Blenniiformes | Tripterygiidae | Ceratobregma helenae | native | Helen's Triplefin | |
| Kurtiformes | Apogonidae | Cercamia eremia | native | Glassy cardinalfish | |
| Mugiliformes | Mugilidae | Cestraeus plicatilis | native | Lobed river mullet | |
| Acanthuriformes | Chaetodontidae | Chaetodon adiergastos | native | Philippine butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon argentatus | native | Asian butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon auriga | native | Threadfin butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon auripes | native | Oriental butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon baronessa | native | Eastern triangular butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon bennetti | native | Bluelashed butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon citrinellus | native | Speckled butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon daedalma | native | Wrought iron butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon ephippium | native | Saddle butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon guentheri | native | Crochet butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon kleinii | native | Sunburst butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon lineolatus | native | Lined butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon lunula | native | Raccoon butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon lunulatus | native | Oval butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon melannotus | native | Blackback butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon mertensii | native | Atoll butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon meyeri | native | Scrawled butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon nippon | native | Japanese butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon octofasciatus | native | Eightband butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon ornatissimus | native | Ornate butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon plebeius | native | Blueblotch butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon punctatofasciatus | native | Spotband butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon quadrimaculatus | native | Fourspot butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon rafflesii | native | Latticed butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon reticulatus | native | Mailed butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon selene | native | Yellow-dotted butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon semeion | native | Dotted butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon speculum | native | Mirror butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon trifascialis | native | Chevron butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon trifasciatus | native | Melon butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon ulietensis | native | Pacific double-saddle butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon unimaculatus | native | Teardrop butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon vagabundus | native | Vagabond butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon wiebeli | native | Hongkong butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon xanthurus | native | Pearlscale butterflyfish | |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus chrysocephalus | native | Orangeface angelfish | |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus mesoleucus | native | Vermiculated angelfish | |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus septentrionalis | native | Bluestriped angelfish | |
| Gonorynchiformes | Chanidae | Chanos chanos | native | Milkfish | |
| Eupercaria/misc | Labridae | Cheilinus chlorourus | native | Floral wrasse | |
| Eupercaria/misc | Labridae | Cheilinus fasciatus | native | Redbreasted wrasse | |
| Eupercaria/misc | Labridae | Cheilinus trilobatus | native | Tripletail wrasse | |
| Eupercaria/misc | Labridae | Cheilinus undulatus | native | Humphead wrasse | |
| Kurtiformes | Apogonidae | Cheilodipterus artus | native | Wolf cardinalfish | |
| Kurtiformes | Apogonidae | Cheilodipterus intermedius | native | Intermediate cardinalfish | |
| Kurtiformes | Apogonidae | Cheilodipterus macrodon | native | Large toothed cardinalfish | |
| Kurtiformes | Apogonidae | Cheilodipterus subulatus | native | ||
| Beloniformes | Exocoetidae | Cheilopogon cyanopterus | native | Margined flyingfish | |
| Beloniformes | Exocoetidae | Cheilopogon spilonotopterus | native | Stained flyingfish | |
| Beloniformes | Exocoetidae | Cheilopogon spilopterus | native | Manyspotted flyingfish | |
| Beloniformes | Exocoetidae | Cheilopogon suttoni | native | Sutton's flyingfish | |
| Beloniformes | Exocoetidae | Cheilopogon unicolor | native | Limpid-wing flyingfish | |
| Ovalentaria/misc | Pomacentridae | Cheiloprion labiatus | native | Big-lip damsel | |
| Acanthuriformes | Chaetodontidae | Chelmon rostratus | native | Copperband butterflyfish | |
| Tetraodontiformes | Tetraodontidae | Chelonodontops patoca | native | Milkspotted puffer | |
| Orectolobiformes | Hemiscylliidae | Chiloscyllium plagiosum | native | Whitespotted bambooshark | |
| Clupeiformes | Chirocentridae | Chirocentrus dorab | native | Dorab wolf-herring | |
| Eupercaria/misc | Scaridae | Chlorurus bowersi | native | Bower's parrotfish | |
| Eupercaria/misc | Scaridae | Chlorurus frontalis | native | Pacific slopehead parrotfish | |
| Eupercaria/misc | Scaridae | Chlorurus japanensis | native | Palecheek parrotfish | |
| Eupercaria/misc | Scaridae | Chlorurus microrhinos | native | Steephead parrots | |
| Eupercaria/misc | Scaridae | Chlorurus oedema | native | Knothead parrotfish | |
| Eupercaria/misc | Scaridae | Chlorurus spilurus | native | Pacific bullethead parrotfish | |
| Eupercaria/misc | Labridae | Choerodon anchorago | native | Orange-dotted tuskfish | |
| Eupercaria/misc | Labridae | Choerodon azurio | native | Azurio tuskfish | |
| Eupercaria/misc | Labridae | Choerodon fasciatus | native | Harlequin tuskfish | |
| Eupercaria/misc | Labridae | Choerodon jordani | native | Jordan's tuskfish | |
| Eupercaria/misc | Labridae | Choerodon robustus | native | Robust tuskfish | |
| Eupercaria/misc | Labridae | Choerodon schoenleinii | native | Blackspot tuskfish | |
| Eupercaria/misc | Labridae | Choerodon zamboangae | native | Purple eyebrowed tuskfish | |
| Perciformes/Serranoidei | Epinephelidae | Chromileptes altivelis | native | Humpback grouper | |
| Ovalentaria/misc | Pomacentridae | Chromis analis | native | Yellow chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis atripectoralis | native | Black-axil chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis chrysura | native | Stout chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis flavomaculata | native | Yellow-spotted chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis fumea | native | Smokey chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis notata | native | Pearl-spot chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis ternatensis | native | Ternate chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis viridis | native | Blue green damselfish | |
| Ovalentaria/misc | Pomacentridae | Chromis weberi | native | Weber's chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis yamakawai | native | Northern yellow-spotted Chromis | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera biocellata | native | Twinspot damselfish | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera caeruleolineata | native | Blueline demoiselle | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera cyanea | native | Sapphire devil | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera glauca | native | Grey demoiselle | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera parasema | native | Goldtail demoiselle | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera rex | native | King demoiselle | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera starcki | native | Starck's demoiselle | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera unimaculata | native | Onespot demoiselle | |
| Eupercaria/misc | Labridae | Cirrhilabrus cyanopleura | native | Blueside wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus exquisitus | native | Exquisite wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus isosceles | native | Pintail fairy-wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus katherinae | native | Katherine's wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus lanceolatus | native | Long-tailed wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus lunatus | native | ||
| Eupercaria/misc | Labridae | Cirrhilabrus rubrimarginatus | native | Red-margined wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus ryukyuensis | native | ||
| Eupercaria/misc | Labridae | Cirrhilabrus temminckii | native | Threadfin wrasse | |
| Centrarchiformes | Cirrhitidae | Cirrhitichthys falco | native | Dwarf hawkfish | |
| Blenniiformes | Blenniidae | Cirripectes castaneus | native | Chestnut eyelash-blenny | |
| Blenniiformes | Blenniidae | Cirripectes filamentosus | native | Filamentous blenny | |
| Blenniiformes | Blenniidae | Cirripectes imitator | native | Imitator blenny | |
| Pleuronectiformes | Pleuronectidae | Cleisthenes pinetorum | native | Sôhachi | |
| Perciformes/Scorpaenoidei | Platycephalidae | Cociella punctata | native | Spotted flathead | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus larvatus | native | Ghost velvetfish | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus possi | native | ||
| Lophiiformes | Ogcocephalidae | Coelophrys brevicaudata | native | ||
| Lophiiformes | Ogcocephalidae | Coelophrys micropus | native | ||
| Gadiformes | Macrouridae | Coelorinchus anatirostris | native | Duckbill grenadier | |
| Gadiformes | Macrouridae | Coelorinchus brevirostris | native | ||
| Gadiformes | Macrouridae | Coelorinchus formosanus | native | Formosa grenadier | |
| Gadiformes | Macrouridae | Coelorinchus japonicus | native | Japanese grenadier | |
| Gadiformes | Macrouridae | Coelorinchus kamoharai | native | Kamohara grenadier | |
| Gadiformes | Macrouridae | Coelorinchus kishinouyei | native | Mugura grenadier | |
| Gadiformes | Macrouridae | Coelorinchus productus | native | Unicorn grenadier | |
| Ovalentaria/misc | Pseudochromidae | Congrogadus subducens | native | Carpet eel-blenny | |
| Acanthuriformes | Chaetodontidae | Coradion altivelis | native | Highfin coralfish | |
| Acanthuriformes | Chaetodontidae | Coradion chrysozonus | native | Goldengirdled coralfish | |
| Acanthuriformes | Chaetodontidae | Coradion melanopus | native | Twospot coralfish | |
| Eupercaria/misc | Labridae | Coris aygula | native | Clown coris | |
| Eupercaria/misc | Labridae | Coris batuensis | native | Batu coris | |
| Eupercaria/misc | Labridae | Coris dorsomacula | native | Pale-barred coris | |
| Eupercaria/misc | Labridae | Coris gaimard | native | African coris | |
| Eupercaria/misc | Labridae | Coris picta | native | Comb wrasse | |
| Carangiformes | Coryphaenidae | Coryphaena equiselis | native | Pompano dolphinfish | |
| Carangiformes | Coryphaenidae | Coryphaena hippurus | native | Common dolphinfish | |
| Syngnathiformes | Syngnathidae | Corythoichthys amplexus | native | Brown-banded pipefish | |
| Syngnathiformes | Syngnathidae | Corythoichthys flavofasciatus | native | Network pipefish | |
| Syngnathiformes | Syngnathidae | Corythoichthys schultzi | native | Schultz's pipefish | |
| Syngnathiformes | Syngnathidae | Cosmocampus banneri | native | Roughridge pipefish | |
| Carangiformes | Carangidae | Craterognathus plagiotaenia | native | Barcheek trevally | |
| Acropomatiformes | Creediidae | Creedia bilineata | native | ||
| Gobiiformes | Gobiidae | Cristatogobius aurimaculatus | native | ||
| Gobiiformes | Gobiidae | Cristatogobius nonatoae | native | ||
| Blenniiformes | Blenniidae | Crossosalarias macrospilus | native | Tripplespot blenny | |
| Gobiiformes | Gobiidae | Cryptocentroides insignis | native | Insignia prawn-goby | |
| Gobiiformes | Gobiidae | Cryptocentrus albidorsus | native | White-backed shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus caeruleomaculatus | native | Blue-speckled prawn-goby | |
| Gobiiformes | Gobiidae | Cryptocentrus cinctus | native | Yellow prawn-goby | |
| Gobiiformes | Gobiidae | Cryptocentrus cyanospilotus | native | Bluespot shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus inexplicatus | native | Inexplicable shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus leptocephalus | native | Pink-speckled shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus leucostictus | native | Saddled prawn-goby | |
| Gobiiformes | Gobiidae | Cryptocentrus nigrocellatus | native | Blackspot shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus strigilliceps | native | Target shrimp goby | |
| Acanthuriformes | Acanthuridae | Ctenochaetus binotatus | native | Twospot surgeonfish | |
| Acanthuriformes | Acanthuridae | Ctenochaetus cyanocheilus | native | Short-tail bristle-tooth | |
| Acanthuriformes | Acanthuridae | Ctenochaetus striatus | native | Striated surgeonfish | |
| Gobiiformes | Gobiidae | Ctenogobiops aurocingulus | native | Gold-streaked prawn-goby | |
| Gobiiformes | Gobiidae | Ctenogobiops crocineus | native | ||
| Gobiiformes | Gobiidae | Ctenogobiops feroculus | native | Sandy prawn-goby | |
| Gobiiformes | Gobiidae | Ctenogobiops pomastictus | native | Gold-specked prawn-goby | |
| Gobiiformes | Gobiidae | Ctenogobiops tangaroai | native | Tangaroa shrimpgoby | |
| Perciformes/Scorpaenoidei | Platycephalidae | Cymbacephalus beauforti | native | Crocodile fish | |
| Pleuronectiformes | Cynoglossidae | Cynoglossus joyneri | native | Red tonguesole | |
| Ovalentaria/misc | Pseudochromidae | Cypho zaps | native | Checkered dottyback | |
| Beloniformes | Exocoetidae | Cypselurus angusticeps | native | Narrowhead flyingfish | |
| Beloniformes | Exocoetidae | Cypselurus opisthopus | native | Black-finned flyingfish | |
| Dactylopteriformes | Dactylopteridae | Dactyloptena orientalis | native | Oriental flying gurnard | |
| Callionymiformes | Callionymidae | Dactylopus dactylopus | native | Fingered dragonet | |
| Ovalentaria/misc | Pomacentridae | Dascyllus aruanus | native | Whitetail dascyllus | |
| Ovalentaria/misc | Pomacentridae | Dascyllus melanurus | native | Blacktail humbug | |
| Ovalentaria/misc | Pomacentridae | Dascyllus reticulatus | native | Reticulate dascyllus | |
| Squaliformes | Centrophoridae | Deania calceus | native | Birdbeak dogfish | |
| Carangiformes | Carangidae | Decapterus kurroides | native | Redtail scad | |
| Carangiformes | Carangidae | Decapterus macarellus | native | Mackerel scad | |
| Carangiformes | Carangidae | Decapterus macrosoma | native | Shortfin scad | |
| Carangiformes | Carangidae | Decapterus russelli | native | Indian scad | |
| Carangiformes | Carangidae | Decapterus tabl | native | Roughear scad | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Dendrochirus biocellatus | native | Twospot turkeyfish | |
| Eupercaria/misc | Sparidae | Dentex abei | native | Yellowfin sea bream | |
| Gobiesociformes | Gobiesocidae | Diademichthys lineatus | native | ||
| Ophidiiformes | Dinematichthyidae | Diancistrus erythraeus | native | Red viviparous brotula | |
| Ophidiiformes | Dinematichthyidae | Diancistrus fuscus | native | Dusky brotulid | |
| Ophidiiformes | Dinematichthyidae | Diancistrus jackrandalli | native | Randall's coralbrotula | |
| Myctophiformes | Myctophidae | Diaphus brachycephalus | native | Short-headed lantern fish | |
| Myctophiformes | Myctophidae | Diaphus fragilis | native | Fragile lantern fish | |
| Myctophiformes | Myctophidae | Diaphus problematicus | native | Problematic lanternfish | |
| Myctophiformes | Myctophidae | Diaphus schmidti | native | ||
| Ophidiiformes | Dinematichthyidae | Dinematichthys iluocoeteoides | native | Yellow pigmy brotula | |
| Tetraodontiformes | Diodontidae | Diodon eydouxii | native | Pelagic porcupinefish | |
| Callionymiformes | Callionymidae | Diplogrammus goramensis | native | Goram dragonet | |
| Callionymiformes | Callionymidae | Diplogrammus xenicus | native | Japanese fold dragonet | |
| Scombriformes | Gempylidae | Diplospinus multistriatus | native | Striped escolar | |
| Ovalentaria/misc | Pomacentridae | Dischistodus melanotus | native | Black-vent damsel | |
| Ovalentaria/misc | Pomacentridae | Dischistodus prosopotaenia | native | Honey-head damsel | |
| Gobiiformes | Gobiidae | Discordipinna filamentosa | native | ||
| Gobiiformes | Gobiidae | Discordipinna griessingeri | native | Spikefin goby | |
| Gobiesociformes | Gobiesocidae | Discotrema crinophilum | native | Crinoid clingfish | |
| Syngnathiformes | Syngnathidae | Doryrhamphus excisus | native | Bluestripe pipefish | |
| Syngnathiformes | Syngnathidae | Doryrhamphus negrosensis | native | Negros pipefish | |
| Acanthuriformes | Drepaneidae | Drepane longimana | native | Concertina fish | |
| Acanthuriformes | Drepaneidae | Drepane punctata | native | Spotted sicklefish | |
| Syngnathiformes | Syngnathidae | Dunckerocampus dactyliophorus | native | Ringed pipefish | |
| Anguilliformes | Muraenidae | Echidna nebulosa | native | Starry moray | |
| Anguilliformes | Muraenidae | Echidna polyzona | native | Barred moray | |
| Gobiiformes | Gobiidae | Echinogobius hayashii | native | Cheek-streaked goby | |
| Blenniiformes | Blenniidae | Ecsenius bicolor | native | Bicolor blenny | |
| Blenniiformes | Blenniidae | Ecsenius lineatus | native | Linear blenny | |
| Blenniiformes | Blenniidae | Ecsenius oculus | native | Ocular blenny | |
| Blenniiformes | Blenniidae | Ecsenius yaeyamaensis | native | Yaeyama blenny | |
| Gobiiformes | Gobiidae | Egglestonichthys fulmen | native | Eggleston’s lightning goby | |
| Carangiformes | Carangidae | Elagatis bipinnulata | native | Rainbow runner | |
| Callionymiformes | Callionymidae | Eleutherochir opercularis | native | Flap-gilled dragonet | |
| Ophidiiformes | Carapidae | Encheliophis boraborensis | native | Pinhead pearlfish | |
| Ophidiiformes | Carapidae | Encheliophis gracilis | native | Graceful pearlfish | |
| Ophidiiformes | Carapidae | Encheliophis homei | native | Silver pearlfish | |
| Ophidiiformes | Carapidae | Encheliophis vermicularis | native | Worm pearlfish | |
| Anguilliformes | Muraenidae | Enchelycore bayeri | native | Bayer's moray | |
| Anguilliformes | Muraenidae | Enchelycore schismatorhynchus | native | White-margined moray | |
| Blenniiformes | Blenniidae | Enchelyurus kraussii | native | Krauss' blenny | |
| Clupeiformes | Engraulidae | Encrasicholina heteroloba | native | Shorthead anchovy | |
| Clupeiformes | Engraulidae | Encrasicholina punctifer | native | Buccaneer anchovy | |
| Clupeiformes | Engraulidae | Engraulis japonicus | native | Japanese anchovy | |
| Pleuronectiformes | Bothidae | Engyprosopon longipelvis | native | ||
| Blenniiformes | Tripterygiidae | Enneapterygius cheni | native | ||
| Blenniiformes | Tripterygiidae | Enneapterygius etheostoma | native | ||
| Blenniiformes | Tripterygiidae | Enneapterygius flavoccipitis | native | Yellownape tripplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius hemimelas | native | Halfblack Triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius minutus | native | ||
| Blenniiformes | Tripterygiidae | Enneapterygius philippinus | native | Minute triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius rubicauda | native | Redtail triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius unimaculatus | native | Onespot triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius vexillarius | native | Blacksaddle triplefin | Blacksaddle triplefin |
| Blenniiformes | Blenniidae | Entomacrodus decussatus | native | Wavy-lined blenny | |
| Blenniiformes | Blenniidae | Entomacrodus niuafoouensis | native | Tattoo-chin rockskipper | |
| Blenniiformes | Blenniidae | Entomacrodus stellifer | native | Stellar rockskipper | |
| Blenniiformes | Blenniidae | Entomacrodus striatus | native | Reef margin blenny | |
| Pleuronectiformes | Pleuronectidae | Eopsetta grigorjewi | native | Shotted halibut | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus coioides | native | Orange-spotted grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus corallicola | native | Coral grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus cyanopodus | native | Speckled blue grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus epistictus | native | Dotted grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus fuscoguttatus | native | Brown-marbled grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus hexagonatus | native | Starspotted grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus howlandi | native | Blacksaddle grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus lanceolatus | native | Giant grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus macrospilos | native | Snubnose grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus maculatus | native | Highfin grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus malabaricus | native | Malabar grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus melanostigma | native | One-blotch grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus merra | native | Honeycomb grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus miliaris | native | Netfin grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus morrhua | native | Comet grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus ongus | native | White-streaked grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus polyphekadion | native | Camouflage grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus radiatus | native | Oblique-banded grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus retouti | native | Red-tipped grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus rivulatus | native | Halfmoon grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus tauvina | native | Greasy grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus tukula | native | Potato grouper | |
| Acanthuriformes | Leiognathidae | Equulites leuciscus | native | Whipfin ponyfish | |
| Eupercaria/misc | Emmelichthyidae | Erythrocles schlegelii | native | Japanese rubyfish | |
| Eupercaria/misc | Emmelichthyidae | Erythrocles scintillans | native | Golden kali kali | |
| Eupercaria/misc | Lutjanidae | Etelis carbunculus | native | Deep-water red snapper | |
| Eupercaria/misc | Lutjanidae | Etelis coruscans | native | Deepwater longtail red snapper | |
| Eupercaria/misc | Lutjanidae | Etelis radiosus | native | Pale snapper | |
| Squaliformes | Etmopteridae | Etmopterus lucifer | native | Blackbelly lanternshark | |
| Squaliformes | Etmopteridae | Etmopterus unicolor | native | Bristled lanternshark | |
| Clupeiformes | Dussumieriidae | Etrumeus micropus | native | ||
| Scombriformes | Bramidae | Eumegistus illustris | native | Brilliant pomfret | |
| Gobiiformes | Gobiidae | Eutaeniichthys gilli | native | ||
| Scombriformes | Scombridae | Euthynnus affinis | native | Kawakawa | |
| Aulopiformes | Evermannellidae | Evermannella indica | native | Indian sabretooth | |
| Gobiiformes | Gobiidae | Eviota afelei | native | Afele's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota ancora | native | Hookcheek dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota bifasciata | native | Twostripe dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota cometa | native | Comet dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota distigma | native | Twospot dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota fallax | native | Twin Dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota fasciola | native | Barred dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota filamentosa | native | Threadfin dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota flavipinnata | native | Yellowfin dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota flebilis | native | Tearful dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota herrei | native | Herre's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota infulata | native | Shouldermark dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota japonica | native | Japanese dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota korechika | native | Korechika's dwarfoby | |
| Gobiiformes | Gobiidae | Eviota lachdeberei | native | Lachdebere's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota latifasciata | native | Brownbanded dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota masudai | native | Masuda's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota melasma | native | Headspot dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota nebulosa | native | Nebulous dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota nigrispina | native | Blackspine dwarfgoby | Nadeshiko-isohaze |
| Gobiiformes | Gobiidae | Eviota occasa | native | Sunset dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota ocellifer | native | Ocellated dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota prasites | native | Hairfin dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota punyit | native | Punyit dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota queenslandica | native | Queensland dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota rubriguttata | native | Redspotfin dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota rubrimaculata | native | Redspot dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota sebreei | native | Sebree's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota shibukawai | native | Shibukawa’s dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota shimadai | native | Shimadai's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota smaragdus | native | Emerald dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota specca | native | Dusted dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota storthynx | native | Storthynx dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota toshiyuki | native | Toshiyuki's dwarfgoby | |
| Scombriformes | Trichiuridae | Evoxymetopon macrophthalmus | native | Bigeye scabbard fish | |
| Scombriformes | Trichiuridae | Evoxymetopon poeyi | native | Poey's scabbardfish | |
| Blenniiformes | Blenniidae | Exallias brevis | native | Leopard blenny | |
| Gobiiformes | Gobiidae | Exyrias belissimus | native | Mud reef-goby | |
| Gobiiformes | Gobiidae | Exyrias puntang | native | Puntang goby | |
| Gobiiformes | Gobiidae | Favonigobius reichei | native | Indo-Pacific tropical sand goby | |
| Carangiformes | Carangidae | Ferdauia ferdau | native | Blue trevally | |
| Carangiformes | Carangidae | Ferdauia orthogrammus | native | Island trevally | |
| Kurtiformes | Apogonidae | Fibramia amboinensis | native | Amboina cardinalfish | |
| Kurtiformes | Apogonidae | Fibramia thermalis | native | Half-barred cardinal | |
| Syngnathiformes | Fistulariidae | Fistularia petimba | native | Red cornetfish | |
| Carangiformes | Carangidae | Flavocaranx bajad | native | Orangespotted trevally | |
| Acanthuriformes | Chaetodontidae | Forcipiger flavissimus | native | Longnose butterfly fish | |
| Kurtiformes | Apogonidae | Fowleria aurita | native | Crosseyed cardinalfish | |
| Kurtiformes | Apogonidae | Fowleria isostigma | native | Dotted cardinalfish | |
| Kurtiformes | Apogonidae | Fowleria marmorata | native | Marbled cardinalfish | |
| Kurtiformes | Apogonidae | Fowleria vaiulae | native | Mottled cardinalfish | |
| Kurtiformes | Apogonidae | Fowleria variegata | native | Variegated cardinalfish | |
| Gobiiformes | Gobiidae | Fusigobius gracilis | native | Slender sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius humeralis | native | Shoulderspot sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius longispinus | native | Orange-spotted sand-goby | |
| Gobiiformes | Gobiidae | Fusigobius maximus | native | Large sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius melacron | native | Blacktip sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius neophytus | native | Common fusegoby | |
| Gobiiformes | Gobiidae | Fusigobius signipinnis | native | Signalfin goby | |
| Carcharhiniformes | Galeocerdonidae | Galeocerdo cuvier | native | Tiger shark | |
| Carcharhiniformes | Pentanchidae | Galeus eastmani | native | Gecko catshark | |
| Carcharhiniformes | Pentanchidae | Galeus longirostris | native | Longnose sawtail cat shark | |
| Acanthuriformes | Leiognathidae | Gazza minuta | native | Toothpony | |
| Acanthuriformes | Leiognathidae | Gazza rhombea | native | Rhomboid toothpony | |
| Scombriformes | Gempylidae | Gempylus serpens | native | Snake mackerel | |
| Acanthuriformes | Pomacanthidae | Genicanthus lamarck | native | Blackstriped angelfish | |
| Acanthuriformes | Pomacanthidae | Genicanthus melanospilos | native | Spotbreast angelfish | |
| Acanthuriformes | Pomacanthidae | Genicanthus semifasciatus | native | Japanese swallow | |
| Acanthuriformes | Pomacanthidae | Genicanthus watanabei | native | Blackedged angelfish | |
| Eupercaria/misc | Gerreidae | Gerres erythrourus | native | Deep-bodied mojarra | |
| Eupercaria/misc | Gerreidae | Gerres filamentosus | native | Whipfin silver-biddy | |
| Eupercaria/misc | Gerreidae | Gerres longirostris | native | Strongspine silver-biddy | |
| Eupercaria/misc | Gerreidae | Gerres macracanthus | native | Longspine silverbiddy | |
| Eupercaria/misc | Gerreidae | Gerres oblongus | native | Slender silver-biddy | |
| Eupercaria/misc | Gerreidae | Gerres oyena | native | Common silver-biddy | |
| Eupercaria/misc | Gerreidae | Gerres ryukyuensis | native | Ryukyu banded silver-biddy | |
| Eupercaria/misc | Gerreidae | Gerres shima | native | Banded silver-biddy | |
| Centrarchiformes | Girellidae | Girella leonina | native | ||
| Gobiiformes | Gobiidae | Gladiogobius brevispinis | native | Short-spined goby | |
| Gobiiformes | Gobiidae | Gladiogobius ensifer | native | Gladiator goby | |
| Gobiiformes | Gobiidae | Glossogobius bicirrhosus | native | Bearded flathead goby | |
| Blenniiformes | Blenniidae | Glyptoparus delicatulus | native | Delicate blenny | |
| Carangiformes | Carangidae | Gnathanodon speciosus | native | Golden trevally | |
| Eupercaria/misc | Lethrinidae | Gnathodentex aureolineatus | native | Striped large-eye bream | |
| Gobiiformes | Gobiidae | Gnatholepis anjerensis | native | Eye-bar goby | |
| Gobiiformes | Gobiidae | Gnatholepis cauerensis | native | Eyebar goby | |
| Gobiiformes | Gobiidae | Gnatholepis yoshinoi | native | Yoshino's goby | |
| Gobiiformes | Gobiidae | Gobiodon albofasciatus | native | Whitelined coral goby | |
| Gobiiformes | Gobiidae | Gobiodon aoyagii | native | ||
| Gobiiformes | Gobiidae | Gobiodon atrangulatus | native | ||
| Gobiiformes | Gobiidae | Gobiodon axillaris | native | Red-striped coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon erythrospilus | native | ||
| Gobiiformes | Gobiidae | Gobiodon heterospilos | native | Head and tailspotted coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon micropus | native | ||
| Gobiiformes | Gobiidae | Gobiodon multilineatus | native | ||
| Gobiiformes | Gobiidae | Gobiodon oculolineatus | native | Eyeline coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon rivulatus | native | Rippled coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon spilophthalmus | native | White-lined coral goby | |
| Gobiiformes | Gobiidae | Gobiodon unicolor | native | Unicolor coralgoby | |
| Gobiiformes | Gobiidae | Gobiopsis arenaria | native | Patchwork barbelgoby | |
| Gobiiformes | Gobiidae | Gobiopsis bravoi | native | Bravo's bearded goby | |
| Gobiiformes | Gobiidae | Gobiopsis liolepis | native | ||
| Gobiiformes | Gobiidae | Gobiopsis quinquecincta | native | Fiveband barbelgoby | |
| Gobiiformes | Kraemeriidae | Gobitrichinotus radiocularis | native | ||
| Anguilliformes | Congridae | Gorgasia preclara | native | Splendid garden eel | |
| Perciformes/Serranoidei | Epinephelidae | Gracila albomarginata | native | Masked grouper | |
| Pleuronectiformes | Bothidae | Grammatobothus polyophthalmus | native | Threespot flounder | |
| Scombriformes | Scombridae | Grammatorcynus bilineatus | native | Double-lined mackerel | Kusarah |
| Perciformes/Serranoidei | Grammistidae | Grammistops ocellatus | native | Ocellate soapfish | |
| Ophidiiformes | Bythitidae | Grammonus yunokawai | native | ||
| Ateleopodiformes | Ateleopodidae | Guentherus katoi | native | ||
| Gobiiformes | Microdesmidae | Gunnellichthys monostigma | native | Onespot wormfish | |
| Gobiiformes | Microdesmidae | Gunnellichthys pleurotaenia | native | Onestripe wormfish | |
| Kurtiformes | Apogonidae | Gymnapogon philippinus | native | Philippine cardinalfish | |
| Kurtiformes | Apogonidae | Gymnapogon urospilotus | native | B-spot cardinalfish | |
| Eupercaria/misc | Lethrinidae | Gymnocranius elongatus | native | Forktail large-eye bream | |
| Eupercaria/misc | Lethrinidae | Gymnocranius euanus | native | Japanese large-eye bream | |
| Eupercaria/misc | Lethrinidae | Gymnocranius grandoculis | native | Blue-lined large-eye bream | |
| Eupercaria/misc | Lethrinidae | Gymnocranius griseus | native | Grey large-eye bream | |
| Eupercaria/misc | Lethrinidae | Gymnocranius microdon | native | Blue-spotted large-eye bream | |
| Anguilliformes | Muraenidae | Gymnomuraena zebra | native | Zebra moray | |
| Scombriformes | Scombridae | Gymnosarda unicolor | native | Dogtooth tuna | |
| Anguilliformes | Muraenidae | Gymnothorax buroensis | native | Vagrant moray | |
| Anguilliformes | Muraenidae | Gymnothorax chilospilus | native | Lipspot moray | |
| Anguilliformes | Muraenidae | Gymnothorax chlamydatus | native | Banded mud moray | Kuruma-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax enigmaticus | native | Enigmatic moray | |
| Anguilliformes | Muraenidae | Gymnothorax fimbriatus | native | Fimbriated moray | |
| Anguilliformes | Muraenidae | Gymnothorax flavimarginatus | native | Yellow-edged moray | |
| Anguilliformes | Muraenidae | Gymnothorax herrei | native | Herre's moray | |
| Anguilliformes | Muraenidae | Gymnothorax javanicus | native | Giant moray | |
| Anguilliformes | Muraenidae | Gymnothorax margaritophorus | native | Blotch-necked moray | |
| Anguilliformes | Muraenidae | Gymnothorax melatremus | native | Dwarf moray | |
| Anguilliformes | Muraenidae | Gymnothorax meleagris | native | Turkey moray | |
| Anguilliformes | Muraenidae | Gymnothorax monochrous | native | Drab moray | |
| Anguilliformes | Muraenidae | Gymnothorax nudivomer | native | Yellowmouth moray | |
| Anguilliformes | Muraenidae | Gymnothorax philippinus | native | Philippines moray | |
| Anguilliformes | Muraenidae | Gymnothorax pictus | native | Paintspotted moray | Ase-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax pindae | native | Pinda moray | |
| Anguilliformes | Muraenidae | Gymnothorax pseudothyrsoideus | native | Highfin moray | |
| Anguilliformes | Muraenidae | Gymnothorax reevesii | native | Reeve's moray | |
| Anguilliformes | Muraenidae | Gymnothorax richardsonii | native | Richardson's moray | |
| Anguilliformes | Muraenidae | Gymnothorax rueppelliae | native | Banded moray | |
| Anguilliformes | Muraenidae | Gymnothorax ryukyuensis | native | ||
| Anguilliformes | Muraenidae | Gymnothorax thyrsoideus | native | Greyface moray | |
| Syngnathiformes | Syngnathidae | Halicampus brocki | native | Brock's pipefish | |
| Syngnathiformes | Syngnathidae | Halicampus mataafae | native | Samoan pipefish | |
| Syngnathiformes | Syngnathidae | Halicampus nitidus | native | Glittering pipefish | |
| Eupercaria/misc | Labridae | Halichoeres argus | native | Argus wrasse | |
| Eupercaria/misc | Labridae | Halichoeres chrysus | native | Canary wrasse | |
| Eupercaria/misc | Labridae | Halichoeres hartzfeldii | native | Hartzfeld's wrasse | |
| Eupercaria/misc | Labridae | Halichoeres hortulanus | native | Checkerboard wrasse | |
| Eupercaria/misc | Labridae | Halichoeres kneri | native | Kner's wrasse | |
| Eupercaria/misc | Labridae | Halichoeres leucurus | native | Greyhead wrasse | |
| Eupercaria/misc | Labridae | Halichoeres melanochir | native | Orangefin wrasse | |
| Eupercaria/misc | Labridae | Halichoeres melanurus | native | Tail-spot wrasse | |
| Eupercaria/misc | Labridae | Halichoeres miniatus | native | Circle-cheek wrasse | |
| Eupercaria/misc | Labridae | Halichoeres orientalis | native | ||
| Eupercaria/misc | Labridae | Halichoeres ornatissimus | native | Ornamented wrasse | |
| Eupercaria/misc | Labridae | Halichoeres prosopeion | native | Twotone wrasse | |
| Eupercaria/misc | Labridae | Halichoeres richmondi | native | Richmond's wrasse | |
| Lophiiformes | Ogcocephalidae | Halieutopsis stellifera | native | ||
| Blenniiformes | Tripterygiidae | Helcogramma aquila | native | Darktail triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma fuscipectoris | native | Fourspot triplefin | Fourspot triplefin |
| Blenniiformes | Tripterygiidae | Helcogramma fuscopinna | native | Blackfin triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma hudsoni | native | Hudson's triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma inclinata | native | Triangle triplefin | Triangle triplefin |
| Blenniiformes | Tripterygiidae | Helcogramma obtusirostris | native | Hotlips triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma striata | native | Tropical striped triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma trigloides | native | Scarf triplefin | |
| Ovalentaria/misc | Pomacentridae | Hemiglyphidodon plagiometopon | native | Lagoon damselfish | |
| Eupercaria/misc | Labridae | Hemigymnus melapterus | native | Blackeye thicklip | |
| Beloniformes | Hemiramphidae | Hemiramphus far | native | Black-barred halfbeak | |
| Acanthuriformes | Chaetodontidae | Hemitaurichthys polylepis | native | Pyramid butterflyfish | |
| Carcharhiniformes | Triakidae | Hemitriakis complicofasciata | native | ||
| Carcharhiniformes | Triakidae | Hemitriakis japanica | native | Japanese topeshark | |
| Acanthuriformes | Chaetodontidae | Heniochus acuminatus | native | Pennant coralfish | |
| Acanthuriformes | Chaetodontidae | Heniochus chrysostomus | native | Threeband pennantfish | |
| Acanthuriformes | Chaetodontidae | Heniochus diphreutes | native | False moorish idol | |
| Acanthuriformes | Chaetodontidae | Heniochus monoceros | native | Masked bannerfish | |
| Acanthuriformes | Chaetodontidae | Heniochus singularius | native | Singular bannerfish | |
| Acanthuriformes | Chaetodontidae | Heniochus varius | native | Horned bannerfish | |
| Hexanchiformes | Hexanchidae | Heptranchias perlo | native | Sharpnose sevengill shark | |
| Clupeiformes | Dorosomatidae | Herklotsichthys quadrimaculatus | native | Bluestripe herring | |
| Gobiiformes | Gobiidae | Hetereleotris exilis | native | ||
| Gobiiformes | Gobiidae | Hetereleotris poecila | native | ||
| Anguilliformes | Congridae | Heteroconger hassi | native | Spotted garden-eel | |
| Anguilliformes | Congridae | Heteroconger polyzona | native | Zebra garden eel | |
| Heterodontiformes | Heterodontidae | Heterodontus japonicus | native | Japanese bullhead shark | |
| Heterodontiformes | Heterodontidae | Heterodontus zebra | native | Zebra bullhead shark | |
| Pleuronectiformes | Soleidae | Heteromycteris japonicus | native | Bamboo sole | |
| Eupercaria/misc | Priacanthidae | Heteropriacanthus cruentatus | native | Glasseye | |
| Hexanchiformes | Hexanchidae | Hexanchus nakamurai | native | Bigeyed sixgill shark | |
| Myliobatiformes | Hexatrygonidae | Hexatrygon bickelli | native | Sixgill stingray | |
| Myliobatiformes | Dasyatidae | Himantura uarnak | native | Honeycomb stingray | |
| Syngnathiformes | Syngnathidae | Hippichthys cyanospilos | native | Blue-spotted pipefish | |
| Syngnathiformes | Syngnathidae | Hippocampus bargibanti | native | Pygmy seahorse | |
| Syngnathiformes | Syngnathidae | Hippocampus kuda | native | Spotted seahorse | |
| Syngnathiformes | Syngnathidae | Hippocampus pontohi | native | Pontoh's pygmy seahorse | |
| Eupercaria/misc | Scaridae | Hipposcarus longiceps | native | Pacific longnose parrotfish | |
| Eupercaria/misc | Labridae | Hologymnosus rhodonotus | native | Redback longface wrasse | |
| Eupercaria/misc | Malacanthidae | Hoplolatilus cuniculus | native | Dusky tilefish | |
| Atheriniformes | Atherinidae | Hypoatherina woodwardi | native | ||
| Beloniformes | Hemiramphidae | Hyporhamphus affinis | native | Tropical halfbeak | |
| Beloniformes | Hemiramphidae | Hyporhamphus dussumieri | native | Dussumier's halfbeak | |
| Beloniformes | Hemiramphidae | Hyporhamphus intermedius | native | Asian pencil halfbeak | |
| Beloniformes | Hemiramphidae | Hyporhamphus yuri | native | Yuri-sayori | |
| Perciformes/Serranoidei | Epinephelidae | Hyporthodus octofasciatus | native | Eightbar grouper | |
| Clupeiformes | Pristigasteridae | Ilisha elongata | native | Elongate ilisha | |
| Eupercaria/misc | Labridae | Iniistius aneitensis | native | Yellowblotch razorfish | |
| Eupercaria/misc | Labridae | Iniistius dea | native | Blackspot razorfish | |
| Eupercaria/misc | Labridae | Iniistius evides | native | ||
| Eupercaria/misc | Labridae | Iniistius melanopus | native | Yellowpatch razorfish | |
| Eupercaria/misc | Labridae | Iniistius pavo | native | Peacock wrasse | |
| Eupercaria/misc | Labridae | Iniistius pentadactylus | native | Fivefinger wrasse | |
| Eupercaria/misc | Labridae | Iniistius twistii | native | Redblotch razorfish | |
| Perciformes/Scorpaenoidei | Synanceiidae | Inimicus didactylus | native | Bearded ghoul | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Iracundus signifer | native | Decoy scorpionfish | |
| Squaliformes | Dalatiidae | Isistius plutodus | native | Largetooth cookiecutter shark | |
| Blenniiformes | Blenniidae | Istiblennius edentulus | native | Rippled rockskipper | |
| Blenniiformes | Blenniidae | Istiblennius lineatus | native | Lined rockskipper | |
| Gobiiformes | Gobiidae | Istigobius campbelli | native | ||
| Gobiiformes | Gobiidae | Istigobius decoratus | native | Decorated goby | |
| Gobiiformes | Gobiidae | Istigobius goldmanni | native | Goldman's goby | |
| Gobiiformes | Gobiidae | Istigobius ornatus | native | Ornate goby | |
| Gobiiformes | Gobiidae | Istigobius rigilius | native | Rigilius goby | |
| Carangiformes | Istiophoridae | Istiompax indica | native | Black marlin | |
| Lamniformes | Lamnidae | Isurus oxyrinchus | native | Shortfin mako | |
| Carangiformes | Istiophoridae | Kajikia audax | native | Striped marlin | |
| Scombriformes | Scombridae | Katsuwonus pelamis | native | Skipjack tuna | |
| Anguilliformes | Chlopsidae | Kaupichthys atronasus | native | Black-nostril false moray | |
| Anguilliformes | Chlopsidae | Kaupichthys diodontus | native | Common false moray | |
| Anguilliformes | Chlopsidae | Kaupichthys hyoproroides | native | False moray | |
| Gobiiformes | Gobiidae | Kelloggella cardinalis | native | Cardinal goby | |
| Gobiiformes | Gobiidae | Kelloggella quindecimfasciata | native | Central goby | |
| Clupeiformes | Dorosomatidae | Konosirus punctatus | native | Dotted gizzard shad | |
| Gobiiformes | Gobiidae | Koumansetta hectori | native | Hector's goby | |
| Gobiiformes | Kraemeriidae | Kraemeria cunicularia | native | Transparent sand dart | |
| Gobiiformes | Kraemeriidae | Kraemeria tongaensis | native | ||
| Centrarchiformes | Kuhliidae | Kuhlia mugil | native | Barred flagtail | |
| Centrarchiformes | Kuhliidae | Kuhlia rupestris | native | Rock flagtail | |
| Centrarchiformes | Kyphosidae | Kyphosus pacificus | native | Pacific drummer | |
| Ovalentaria/misc | Pseudochromidae | Labracinus cyclophthalmus | native | Fire-tail devil | |
| Eupercaria/misc | Labridae | Labrichthys unilineatus | native | Tubelip wrasse | |
| Eupercaria/misc | Labridae | Labropsis manabei | native | Northern tubelip | |
| Myctophiformes | Myctophidae | Lampadena luminosa | native | Luminous lanternfish | |
| Eupercaria/misc | Sciaenidae | Larimichthys polyactis | native | Yellow croaker | |
| Acanthuriformes | Leiognathidae | Leiognathus equula | native | Common ponyfish | |
| Anguilliformes | Ophichthidae | Leiuranus semicinctus | native | Saddled snake-eel | |
| Scombriformes | Gempylidae | Lepidocybium flavobrunneum | native | Escolar | |
| Ovalentaria/misc | Pomacentridae | Lepidozygus tapeinosoma | native | Fusilier damselfish | |
| Aulopiformes | Aulopidae | Leptaulopus damasi | native | ||
| Alepocephaliformes | Alepocephalidae | Leptoderma retropinna | native | ||
| Eupercaria/misc | Scaridae | Leptoscarus vaigiensis | native | Marbled parrotfish | |
| Scombriformes | Trichiuridae | Lepturacanthus savala | native | Savalai hairtail | |
| Eupercaria/misc | Lethrinidae | Lethrinus amboinensis | native | Ambon emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus atkinsoni | native | Pacific yellowtail emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus erythracanthus | native | Orange-spotted emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus genivittatus | native | Longspine emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus haematopterus | native | Chinese emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus lentjan | native | Pink ear emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus microdon | native | Smalltooth emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus miniatus | native | Trumpet emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus nebulosus | native | Spangled emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus obsoletus | native | Orange-striped emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus olivaceus | native | Longface emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus ornatus | native | Ornate emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus ravus | native | Drab emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus reticulatus | native | Red snout emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus rubrioperculatus | native | Spotcheek emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus semicinctus | native | Black blotch emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus variegatus | native | Slender emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus xanthochilus | native | Yellowlip emperor | |
| Acropomatiformes | Creediidae | Limnichthys orientalis | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma aragai | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma erythraeum | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma japonicum | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma lemniscatum | native | Ribbon basslet | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma lunulatum | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma maculatum | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma susumi | native | Meteor perch | |
| Eupercaria/misc | Lutjanidae | Lipocheilus carnolabrum | native | Tang's snapper | |
| Gobiiformes | Gobiidae | Lotilia klausewitzi | native | Dancer shrimp goby | |
| Ovalentaria/misc | Pseudochromidae | Lubbockichthys tanakai | native | Tanaka's dottyback | |
| Gobiiformes | Gobiidae | Lubricogobius dinah | native | Dinah's goby | |
| Gobiiformes | Gobiidae | Lubricogobius ornatus | native | Ornate slippery goby | |
| Gobiiformes | Gobiidae | Luciogobius elongatus | native | ||
| Eupercaria/misc | Lutjanidae | Lutjanus argentimaculatus | native | Mangrove red snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus bohar | native | Two-spot red snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus boutton | native | Moluccan snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus decussatus | native | Checkered snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus erythropterus | native | Crimson snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus fulviflamma | native | Dory snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus fulvus | native | Blacktail snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus gibbus | native | Humpback red snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus goldiei | native | Papuan black snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus johnii | native | John's snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus kasmira | native | Common bluestripe snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus lutjanus | native | Bigeye snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus malabaricus | native | Malabar blood snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus monostigma | native | One-spot snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus quinquelineatus | native | Five-lined snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus rivulatus | native | Blubberlip snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus russellii | native | Russell's snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus sebae | native | Emperor red snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus stellatus | native | Star snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus vitta | native | Brownstripe red snapper | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys ryukyuensis | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodapus microchir | native | ||
| Eupercaria/misc | Lutjanidae | Macolor macularis | native | Midnight snapper | |
| Eupercaria/misc | Lutjanidae | Macolor niger | native | Black and white snapper | |
| Gobiiformes | Gobiidae | Macrodontogobius wilburi | native | Largetooth goby | |
| Eupercaria/misc | Labridae | Macropharyngodon meleagris | native | Blackspotted wrasse | |
| Eupercaria/misc | Labridae | Macropharyngodon moyeri | native | ||
| Eupercaria/misc | Labridae | Macropharyngodon negrosensis | native | Yellowspotted wrasse | |
| Carangiformes | Istiophoridae | Makaira mazara | native | Indo-Pacific blue marlin | |
| Eupercaria/misc | Malacanthidae | Malacanthus brevirostris | native | Quakerfish | |
| Eupercaria/misc | Malacanthidae | Malacanthus latovittatus | native | Blue blanquillo | |
| Lophiiformes | Ogcocephalidae | Malthopsis gigas | native | Giant triangular batfish | |
| Carangiformes | Carangidae | Megalaspis cordyla | native | Torpedo scad | |
| Perciformes/Serranoidei | Anthiadidae | Meganthias kingyo | native | Itoman-okingyo | |
| Blenniiformes | Blenniidae | Meiacanthus atrodorsalis | native | Forktail blenny | |
| Blenniiformes | Blenniidae | Meiacanthus ditrema | native | One-striped poison-fang blenny | |
| Blenniiformes | Blenniidae | Meiacanthus grammistes | native | Striped poison-fang blenny | |
| Tetraodontiformes | Balistidae | Melichthys niger | native | Black triggerfish | |
| Blenniiformes | Blenniidae | Mimoblennius atrocinctus | native | Spotted and barred blenny | |
| Gobiiformes | Gobiidae | Minysicya caudimaculata | native | Blackspot minigoby | |
| Perciformes/Serranoidei | Anthiadidae | Mirolabrichthys pascalus | native | Amethyst anthias | |
| Tetraodontiformes | Monacanthidae | Monacanthus chinensis | native | Fan-bellied leatherjacket | |
| Eupercaria/misc | Monodactylidae | Monodactylus argenteus | native | Silver moony | |
| Saccopharyngiformes | Monognathidae | Monognathus ozawai | native | ||
| Eupercaria/misc | Lethrinidae | Monotaxis grandoculis | native | Humpnose big-eye bream | |
| Anguilliformes | Moringuidae | Moringua abbreviata | native | ||
| Anguilliformes | Moringuidae | Moringua bicolor | native | Bicolor spaghetti eel | |
| Anguilliformes | Moringuidae | Moringua ferruginea | native | Rusty spaghetti eel | |
| Anguilliformes | Moringuidae | Moringua javanica | native | Java spaghetti eel | |
| Anguilliformes | Moringuidae | Moringua microchir | native | Lesser thrush eel | |
| Gobiiformes | Gobiidae | Mugilogobius abei | native | ||
| Gobiiformes | Gobiidae | Mugilogobius chulae | native | Yellowstripe goby | |
| Gobiiformes | Gobiidae | Mugilogobius fuscus | native | ||
| Gobiiformes | Gobiidae | Mugilogobius notospilus | native | Freshwater mangrovegoby | |
| Gobiiformes | Gobiidae | Mugilogobius tagala | native | ||
| Mulliformes | Mullidae | Mulloidichthys flavolineatus | native | Yellowstripe goatfish | |
| Mulliformes | Mullidae | Mulloidichthys pfluegeri | native | Orange goatfish | |
| Mulliformes | Mullidae | Mulloidichthys vanicolensis | native | Yellowfin goatfish | |
| Anguilliformes | Ophichthidae | Muraenichthys schultzei | native | Maimed snake eel | |
| Carcharhiniformes | Triakidae | Mustelus manazo | native | Starspotted smooth-hound | |
| Gobiiformes | Gobiidae | Myersina macrostoma | native | Bigmouth shrimpgoby | |
| Gobiiformes | Gobiidae | Myersina nigrivirgata | native | Black-line shrimp-goby | |
| Anguilliformes | Ophichthidae | Myrichthys colubrinus | native | Harlequin snake eel | |
| Holocentriformes | Holocentridae | Myripristis adusta | native | Shadowfin soldierfish | |
| Holocentriformes | Holocentridae | Myripristis amaena | native | Brick soldierfish | |
| Holocentriformes | Holocentridae | Myripristis berndti | native | Blotcheye soldierfish | |
| Holocentriformes | Holocentridae | Myripristis botche | native | Blacktip soldierfish | |
| Holocentriformes | Holocentridae | Myripristis greenfieldi | native | ||
| Holocentriformes | Holocentridae | Myripristis hexagona | native | Doubletooth soldierfish | |
| Holocentriformes | Holocentridae | Myripristis murdjan | native | Pinecone soldierfish | |
| Holocentriformes | Holocentridae | Myripristis pralinia | native | Scarlet soldierfish | |
| Holocentriformes | Holocentridae | Myripristis violacea | native | Lattice soldierfish | |
| Blenniiformes | Blenniidae | Nannosalarias nativitatis | native | Pygmy blenny | |
| Alepocephaliformes | Alepocephalidae | Narcetes kamoharai | native | ||
| Acanthuriformes | Acanthuridae | Naso annulatus | native | Whitemargin unicornfish | |
| Acanthuriformes | Acanthuridae | Naso brachycentron | native | Humpback unicornfish | |
| Acanthuriformes | Acanthuridae | Naso brevirostris | native | Spotted unicornfish | |
| Acanthuriformes | Acanthuridae | Naso fageni | native | Horseface unicornfish | |
| Acanthuriformes | Acanthuridae | Naso hexacanthus | native | Sleek unicornfish | |
| Acanthuriformes | Acanthuridae | Naso lituratus | native | Orangespine unicornfish | |
| Acanthuriformes | Acanthuridae | Naso lopezi | native | Elongate unicornfish | |
| Acanthuriformes | Acanthuridae | Naso maculatus | native | ||
| Acanthuriformes | Acanthuridae | Naso thynnoides | native | Oneknife unicornfish | |
| Acanthuriformes | Acanthuridae | Naso tonganus | native | Bulbnose unicornfish | |
| Acanthuriformes | Acanthuridae | Naso unicornis | native | Bluespine unicornfish | |
| Acanthuriformes | Acanthuridae | Naso vlamingii | native | Bignose unicornfish | |
| Carangiformes | Carangidae | Naucrates ductor | native | Pilotfish | |
| Gobiiformes | Microdesmidae | Navigobius dewa | native | ||
| Scombriformes | Gempylidae | Nealotus tripes | native | Black snake mackerel | |
| Kurtiformes | Apogonidae | Neamia articycla | native | Circular cardinalfish | |
| Kurtiformes | Apogonidae | Neamia octospina | native | Eightspine cardinalfish | |
| Orectolobiformes | Ginglymostomatidae | Nebrius ferrugineus | native | Tawny nurse shark | |
| Kurtiformes | Apogonidae | Nectamia bandanensis | native | Bigeye cardinalfish | |
| Kurtiformes | Apogonidae | Nectamia fusca | native | Ghost cardinalfish | |
| Kurtiformes | Apogonidae | Nectamia savayensis | native | Samoan cardinalfish | |
| Carcharhiniformes | Carcharhinidae | Negaprion acutidens | native | Sicklefin lemon shark | |
| Perciformes/Serranoidei | Anthiadidae | Nemanthias bicolor | native | Bicolor anthias | |
| Perciformes/Serranoidei | Anthiadidae | Nemanthias dispar | native | Peach fairy basslet | |
| Clupeiformes | Dorosomatidae | Nematalosa come | native | Western Pacific gizzard shad | |
| Clupeiformes | Dorosomatidae | Nematalosa japonica | native | Japanese gizzard shad | |
| Gobiiformes | Microdesmidae | Nemateleotris decora | native | Elegant firefish | |
| Gobiiformes | Microdesmidae | Nemateleotris magnifica | native | Fire goby | |
| Eupercaria/misc | Nemipteridae | Nemipterus aurora | native | Dawn threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus bathybius | native | Yellowbelly threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus furcosus | native | Fork-tailed threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus japonicus | native | Japanese threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus thosaporni | native | Palefin threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus virgatus | native | Golden threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus zysron | native | Slender threadfin bream | |
| Centrarchiformes | Cirrhitidae | Neocirrhites armatus | native | Flame hawkfish | |
| Scombriformes | Gempylidae | Neoepinnula orientalis | native | Sackfish | |
| Ovalentaria/misc | Pomacentridae | Neoglyphidodon melas | native | Bowtie damselfish | |
| Ovalentaria/misc | Pomacentridae | Neoglyphidodon nigroris | native | Black-and-gold chromis | |
| Holocentriformes | Holocentridae | Neoniphon argenteus | native | Clearfin squirrelfish | |
| Holocentriformes | Holocentridae | Neoniphon opercularis | native | Blackfin squirrelfish | |
| Ovalentaria/misc | Pomacentridae | Neopomacentrus cyanomos | native | Regal demoiselle | |
| Ovalentaria/misc | Pomacentridae | Neopomacentrus taeniurus | native | Freshwater demoiselle | |
| Gadiformes | Macrouridae | Nezumia condylura | native | Japanese pugnose grenadier | |
| Gadiformes | Macrouridae | Nezumia propinqua | native | Aloha grenadier | |
| Gadiformes | Macrouridae | Nezumia proxima | native | Short-tail grenadier | |
| Eupercaria/misc | Labridae | Novaculichthys taeniourus | native | Rockmover wrasse | |
| Eupercaria/misc | Labridae | Novaculoides macrolepidotus | native | Seagrass wrasse | |
| Gobiiformes | Gobiidae | Obliquogobius cirrifer | native | ||
| Gobiiformes | Gobiidae | Obliquogobius fulvostriatus | native | ||
| Gobiiformes | Gobiidae | Obliquogobius megalops | native | ||
| Perciformes/Serranoidei | Anthiadidae | Odontanthias flagris | native | ||
| Perciformes/Serranoidei | Anthiadidae | Odontanthias katayamai | native | ||
| Perciformes/Serranoidei | Anthiadidae | Odontanthias rhodopeplus | native | ||
| Gobiiformes | Gobiidae | Oligolepis acutipennis | native | Sharptail goby | |
| Blenniiformes | Blenniidae | Omobranchus elongatus | native | Cloister blenny | |
| Blenniiformes | Blenniidae | Omobranchus ferox | native | Gossamer blenny | |
| Blenniiformes | Blenniidae | Omox biporos | native | Omox blenny | |
| Perciformes/Scorpaenoidei | Platycephalidae | Onigocia bimaculata | native | Two-spotted flathead | |
| Ophidiiformes | Carapidae | Onuxodon fowleri | native | Fowler's pearlfish | |
| Anguilliformes | Ophichthidae | Ophichthus erabo | native | Blotched snake-eel | |
| Gobiiformes | Butidae | Ophiocara porocephala | native | Northern mud gudgeon | |
| Ovalentaria/misc | Opistognathidae | Opistognathus castelnaui | native | Castelnau's jawfish | |
| Ovalentaria/misc | Opistognathidae | Opistognathus decorus | native | Tattooedj jawfish | Irezumi-amadai |
| Ovalentaria/misc | Opistognathidae | Opistognathus variabilis | native | Variable jawfish | |
| Gobiiformes | Gobiidae | Oplopomops diacanthus | native | Hole goby | |
| Gobiiformes | Gobiidae | Oplopomus oplopomus | native | Spinecheek goby | |
| Holocentriformes | Holocentridae | Ostichthys archiepiscopus | native | Straighthead soldierfish | |
| Holocentriformes | Holocentridae | Ostichthys hypsipterygion | native | Highfin soldierfish | |
| Holocentriformes | Holocentridae | Ostichthys kaianus | native | Deepwater soldierfish | |
| Kurtiformes | Apogonidae | Ostorhinchus angustatus | native | Broadstriped cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus cheni | native | ||
| Kurtiformes | Apogonidae | Ostorhinchus chrysotaenia | native | Yellowlined cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus compressus | native | Ochre-striped cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus cookii | native | Cook's cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus cyanosoma | native | Yellowstriped cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus endekataenia | native | Candystripe cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus fasciatus | native | Broadbanded cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus ishigakiensis | native | ||
| Kurtiformes | Apogonidae | Ostorhinchus nigrofasciatus | native | Blackstripe cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus parvulus | native | ||
| Kurtiformes | Apogonidae | Ostorhinchus rubrimacula | native | Rubyspot cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus sealei | native | Seale's cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus selas | native | Meteor cardinalfish | |
| Tetraodontiformes | Ostraciidae | Ostracion cubicum | native | Yellow boxfish | |
| Eupercaria/misc | Labridae | Oxycheilinus celebicus | native | Celebes wrasse | |
| Eupercaria/misc | Labridae | Oxycheilinus digramma | native | Cheeklined wrasse | |
| Eupercaria/misc | Labridae | Oxycheilinus orientalis | native | Oriental maori wrasse | |
| Eupercaria/misc | Labridae | Oxycheilinus unifasciatus | native | Ringtail maori wrasse | |
| Tetraodontiformes | Monacanthidae | Oxymonacanthus longirostris | native | Harlequin filefish | |
| Gobiiformes | Gobiidae | Oxyurichthys ophthalmonema | native | Eyebrow goby | |
| Gobiiformes | Gobiidae | Oxyurichthys papuensis | native | Frogface goby | |
| Gobiiformes | Gobiidae | Palutrus meteori | native | Meteor goby | |
| Gobiiformes | Gobiidae | Palutrus reticularis | native | ||
| Gobiiformes | Gobiidae | Pandaka lidwilli | native | Lidwill's dwarfgoby | |
| Gobiiformes | Gobiidae | Pandaka trimaculata | native | ||
| Eupercaria/misc | Lutjanidae | Paracaesio caerulea | native | Japanese snapper | |
| Eupercaria/misc | Lutjanidae | Paracaesio kusakarii | native | Saddle-back snapper | |
| Eupercaria/misc | Lutjanidae | Paracaesio sordida | native | Dirty ordure snapper | |
| Eupercaria/misc | Lutjanidae | Paracaesio stonei | native | Cocoa snapper | |
| Eupercaria/misc | Lutjanidae | Paracaesio xanthura | native | Yellowtail blue snapper | |
| Acanthuriformes | Acanthuridae | Paracanthurus hepatus | native | Palette surgeonfish | |
| Acanthuriformes | Chaetodontidae | Parachaetodon ocellatus | native | Sixspine butterflyfish | |
| Eupercaria/misc | Labridae | Paracheilinus filamentosus | native | Filamentous wrasse | |
| Eupercaria/misc | Labridae | Paracheilinus lineopunctatus | native | Spot-lined flasher | |
| Gobiiformes | Gobiidae | Paragobiodon echinocephalus | native | Redhead goby | |
| Gobiiformes | Gobiidae | Paragobiodon kasaii | native | ||
| Gobiiformes | Gobiidae | Paragobiodon lacunicolus | native | Blackfin coral goby | |
| Gobiiformes | Gobiidae | Paragobiodon melanosoma | native | Dark coral goby | |
| Gobiiformes | Gobiidae | Paragobiodon modestus | native | Warthead goby | |
| Gobiiformes | Gobiidae | Paragobiodon xanthosoma | native | Emerald coral goby | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis basimaculata | native | ||
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis clathrata | native | Latticed sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis cylindrica | native | Cylindrical sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis hexophtalma | native | Speckled sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis millepunctata | native | Black dotted sand perch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis multiplicata | native | Redbarred sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis pacifica | native | ||
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis tetracantha | native | Reticulated sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis xanthozona | native | Yellowbar sandperch | |
| Pleuronectiformes | Cynoglossidae | Paraplagusia bilineata | native | Doublelined tonguesole | |
| Eupercaria/misc | Nemipteridae | Parascolopsis inermis | native | Unarmed dwarf monocle bream | |
| Eupercaria/misc | Nemipteridae | Parascolopsis tosensis | native | Tosa dwarf monocle bream | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena aurita | native | Golden scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena maculipinnis | native | ||
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena mcadamsi | native | McAdam's scorpionfish | |
| Carangiformes | Carangidae | Parastromateus niger | native | Black pomfret | |
| Pleuronectiformes | Soleidae | Pardachirus pavoninus | native | Peacock sole | |
| Blenniiformes | Blenniidae | Parenchelyurus hepburni | native | Hepburn's blenny | |
| Gobiiformes | Microdesmidae | Parioglossus caeruleolineatus | native | ||
| Gobiiformes | Microdesmidae | Parioglossus dotui | native | ||
| Gobiiformes | Microdesmidae | Parioglossus formosus | native | Beautiful hover goby | |
| Gobiiformes | Microdesmidae | Parioglossus lineatus | native | Lined hover goby | |
| Gobiiformes | Microdesmidae | Parioglossus palustris | native | Borneo hoverer | |
| Gobiiformes | Microdesmidae | Parioglossus rainfordi | native | Rainford's dartfish | |
| Gobiiformes | Microdesmidae | Parioglossus raoi | native | Rao's hover goby | |
| Gobiiformes | Microdesmidae | Parioglossus taeniatus | native | Taeniatus dartfish | |
| Gobiiformes | Gobiidae | Parkraemeria rhinoceros | native | ||
| Gobiiformes | Gobiidae | Parkraemeria saltator | native | ||
| Carcharhiniformes | Pentanchidae | Parmaturus pilosus | native | Salamander shark | |
| Mulliformes | Mullidae | Parupeneus barberinoides | native | Bicolor goatfish | |
| Mulliformes | Mullidae | Parupeneus ciliatus | native | Whitesaddle goatfish | |
| Mulliformes | Mullidae | Parupeneus crassilabris | native | Two-banded goatfish | |
| Mulliformes | Mullidae | Parupeneus cyclostomus | native | Gold-saddle goatfish | |
| Mulliformes | Mullidae | Parupeneus heptacanthus | native | Cinnabar goatfish | |
| Mulliformes | Mullidae | Parupeneus indicus | native | Indian goatfish | |
| Mulliformes | Mullidae | Parupeneus multifasciatus | native | Manybar goatfish | |
| Mulliformes | Mullidae | Parupeneus pleurostigma | native | Sidespot goatfish | |
| Mulliformes | Mullidae | Parupeneus spilurus | native | Blackspot goatfish | |
| Acropomatiformes | Pempheridae | Pempheris japonica | native | ||
| Acropomatiformes | Pempheridae | Pempheris oualensis | native | Blackspot sweeper | |
| Ophidiiformes | Ophidiidae | Penopus japonicus | native | ||
| Acropomatiformes | Pentacerotidae | Pentaceros japonicus | native | Japanese armorhead | |
| Eupercaria/misc | Nemipteridae | Pentapodus aureofasciatus | native | Yellowstripe threadfin bream | |
| Eupercaria/misc | Nemipteridae | Pentapodus caninus | native | Small-toothed whiptail | |
| Eupercaria/misc | Nemipteridae | Pentapodus nagasakiensis | native | Japanese whiptail | |
| Eupercaria/misc | Gerreidae | Pentaprion longimanus | native | Longfin mojarra | |
| Gobiiformes | Oxudercidae | Periophthalmus argentilineatus | native | Barred mudskipper | |
| Tetraodontiformes | Monacanthidae | Pervagor aspricaudus | native | Orangetail filefish | |
| Tetraodontiformes | Monacanthidae | Pervagor janthinosoma | native | Blackbar filefish | |
| Tetraodontiformes | Monacanthidae | Pervagor melanocephalus | native | Redtail filefish | |
| Tetraodontiformes | Monacanthidae | Pervagor nigrolineatus | native | Blacklined filefish | |
| Blenniiformes | Blenniidae | Petroscirtes mitratus | native | Floral blenny | |
| Blenniiformes | Blenniidae | Petroscirtes variabilis | native | Variable sabretooth blenny | |
| Gobiiformes | Gobiidae | Phoxacromion kaneharai | native | ||
| Syngnathiformes | Syngnathidae | Phoxocampus belcheri | native | Rock pipefish | |
| Syngnathiformes | Syngnathidae | Phoxocampus tetrophthalmus | native | Trunk-barred pipefish | |
| Anguilliformes | Ophichthidae | Phyllophichthus xenodontus | native | Flappy snake-eel | |
| Gadiformes | Moridae | Physiculus japonicus | native | Japanese codling | |
| Ovalentaria/misc | Pseudochromidae | Pictichromis porphyrea | native | Magenta dottyback | |
| Eupercaria/misc | Lutjanidae | Pinjalo lewisi | native | Slender pinjalo | |
| Blenniiformes | Blenniidae | Plagiotremus laudandus | native | Bicolour fangblenny | |
| Blenniiformes | Blenniidae | Plagiotremus rhinorhynchos | native | Bluestriped fangblenny | |
| Mugiliformes | Mugilidae | Planiliza macrolepis | native | Largescale mullet | |
| Mugiliformes | Mugilidae | Planiliza melinoptera | native | Otomebora mullet | |
| Acanthuriformes | Ephippidae | Platax pinnatus | native | Dusky batfish | |
| Acanthuriformes | Ephippidae | Platax teira | native | Longfin batfish | |
| Carangiformes | Carangidae | Platycaranx chrysophrys | native | Longnose trevally | |
| Carangiformes | Carangidae | Platycaranx malabaricus | native | Malabar trevally | |
| Perciformes/Scorpaenoidei | Platycephalidae | Platycephalus indicus | native | Bartail flathead | |
| Osmeriformes | Plecoglossidae | Plecoglossus altivelis | native | Ayu sweetfish | |
| Eupercaria/misc | Haemulidae | Plectorhinchus albovittatus | native | Two-striped sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus chaetodonoides | native | Harlequin sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus chrysotaenia | native | Yellow-striped sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus diagrammus | native | Striped sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus gibbosus | native | Harry hotlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus lessonii | native | Lesson's thicklip | |
| Eupercaria/misc | Haemulidae | Plectorhinchus lineatus | native | Yellowbanded sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus schotaf | native | Minstrel sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus vittatus | native | Indian Ocean oriental sweetlips | |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias kamii | native | Kami's perchlet | |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias longimanus | native | Longfin perchlet | |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias sagamiensis | native | ||
| Perciformes/Serranoidei | Anthiadidae | Plectranthias yamakawai | native | ||
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon altus | native | Japanese gregory | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon fasciolatus | native | Pacific gregory | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon imparipennis | native | Brighteye damselfish | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon johnstonianus | native | Johnston Island damsel | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon obreptus | native | Western gregory | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon phoenixensis | native | Phoenix devil | |
| Perciformes/Serranoidei | Epinephelidae | Plectropomus areolatus | native | Squaretail coralgrouper | |
| Perciformes/Serranoidei | Epinephelidae | Plectropomus laevis | native | Blacksaddled coralgrouper | |
| Myliobatiformes | Plesiobatidae | Plesiobatis daviesi | native | Deep-water stingray | |
| Ovalentaria/misc | Plesiopidae | Plesiops cephalotaenia | native | Headstripe longfin | |
| Ovalentaria/misc | Plesiopidae | Plesiops coeruleolineatus | native | Crimsontip longfin | |
| Ovalentaria/misc | Plesiopidae | Plesiops corallicola | native | Bluegill longfin | |
| Ovalentaria/misc | Plesiopidae | Plesiops oxycephalus | native | Sharp-nosed longfin | |
| Ovalentaria/misc | Plesiopidae | Plesiops verecundus | native | Redtip longfin | |
| Gobiiformes | Gobiidae | Pleurosicya bilobata | native | Bilobed ghost goby | |
| Gobiiformes | Gobiidae | Pleurosicya coerulea | native | Blue coral ghost goby | |
| Gobiiformes | Gobiidae | Pleurosicya fringilla | native | Staghorn ghostgoby | |
| Gobiiformes | Gobiidae | Pleurosicya micheli | native | Michel's ghost goby | |
| Gobiiformes | Gobiidae | Pleurosicya muscarum | native | Ghost goby | |
| Perciformes/Serranoidei | Grammistidae | Pogonoperca punctata | native | ||
| Carangaria/misc | Polynemidae | Polydactylus plebeius | native | Striped threadfin | |
| Acanthuriformes | Pomacanthidae | Pomacanthus annularis | native | Bluering angelfish | |
| Acanthuriformes | Pomacanthidae | Pomacanthus imperator | native | Emperor angelfish | |
| Acanthuriformes | Pomacanthidae | Pomacanthus navarchus | native | Bluegirdled angelfish | |
| Acanthuriformes | Pomacanthidae | Pomacanthus semicirculatus | native | Semicircle angelfish | |
| Acanthuriformes | Pomacanthidae | Pomacanthus sexstriatus | native | Sixbar angelfish | |
| Acanthuriformes | Pomacanthidae | Pomacanthus xanthometopon | native | Yellowface angelfish | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus alexanderae | native | Alexander's damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus amboinensis | native | Ambon damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus bankanensis | native | Speckled damselfish | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus brachialis | native | Charcoal damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus chrysurus | native | Whitetail damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus coelestis | native | Neon damselfish | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus lepidogenys | native | Scaly damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus moluccensis | native | Lemon damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus nigromarginatus | native | Blackmargined damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus philippinus | native | Philippine damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus simsiang | native | Blueback damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus taeniometopon | native | Brackish damsel | |
| Ovalentaria/misc | Pomacentridae | Pomachromis richardsoni | native | Richardson's reef-damsel | |
| Eupercaria/misc | Haemulidae | Pomadasys quadrilineatus | native | Yellow-lined grunter | |
| Eupercaria/misc | Priacanthidae | Priacanthus zaiserae | native | Miyake bigeye | |
| Gobiiformes | Gobiidae | Priolepis cincta | native | Banded reef goby | |
| Gobiiformes | Gobiidae | Priolepis inhaca | native | Brick goby | |
| Gobiiformes | Gobiidae | Priolepis semidoliata | native | Half-barred goby | |
| Carcharhiniformes | Carcharhinidae | Prionace glauca | native | Blue shark | |
| Acanthuriformes | Acanthuridae | Prionurus scalprum | native | Scalpel sawtail | |
| Kurtiformes | Apogonidae | Pristiapogon exostigma | native | Narrowstripe cardinalfish | |
| Kurtiformes | Apogonidae | Pristiapogon fraenatus | native | Bridled cardinalfish | |
| Kurtiformes | Apogonidae | Pristicon rufus | native | Rufus cardinalfish | |
| Kurtiformes | Apogonidae | Pristicon trimaculatus | native | Three-spot cardinalfish | |
| Eupercaria/misc | Priacanthidae | Pristigenys meyeri | native | ||
| Eupercaria/misc | Lutjanidae | Pristipomoides argyrogrammicus | native | Ornate jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides auricilla | native | Goldflag jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides filamentosus | native | Crimson jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides flavipinnis | native | Golden eye jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides multidens | native | Goldbanded jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides sieboldii | native | Lavender jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides typus | native | Sharptooth jobfish | |
| Eupercaria/misc | Lutjanidae | Pristipomoides zonatus | native | Oblique-banded snapper | |
| Ovalentaria/misc | Pomacentridae | Pristotis obtusirostris | native | Gulf damselfish | |
| Beloniformes | Exocoetidae | Prognichthys brevipinnis | native | Shortfin flyingfish | |
| Scombriformes | Gempylidae | Promethichthys prometheus | native | Roudi escolar | |
| Carcharhiniformes | Proscylliidae | Proscyllium habereri | native | Graceful catshark | |
| Gobiiformes | Gobiidae | Psammogobius biocellatus | native | Sleepy goby | |
| Carangaria/misc | Latidae | Psammoperca waigiensis | native | Waigieu seaperch | |
| Kurtiformes | Apogonidae | Pseudamia gelatinosa | native | Gelatinous cardinalfish | |
| Kurtiformes | Apogonidae | Pseudamia zonata | native | Paddlefish cardinalfish | |
| Kurtiformes | Apogonidae | Pseudamiops gracilicauda | native | Graceful-tailed cardinalfish | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias fasciatus | native | One-stripe anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias hypselosoma | native | Stocky anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias luzonensis | native | Yellowlined anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias pleurotaenia | native | Square-spot fairy basslet | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias randalli | native | Randall's fairy basslet | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias taira | native | ||
| Anguilliformes | Muraenidae | Pseudechidna brummeri | native | White ribbon eel | |
| Carangiformes | Carangidae | Pseudocaranx dentex | native | White trevally | |
| Eupercaria/misc | Labridae | Pseudocheilinus hexataenia | native | Sixline wrasse | |
| Eupercaria/misc | Labridae | Pseudocheilinus ocellatus | native | Whitebarred pink wrasse | |
| Eupercaria/misc | Labridae | Pseudocheilinus octotaenia | native | Eight-lined wrasse | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis cyanotaenia | native | Surge dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis fuscus | native | Brown dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis luteus | native | Orange dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis marshallensis | native | Marshall Is. dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis striatus | native | Striated dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis tapeinosoma | native | Blackmargin dottyback | |
| Eupercaria/misc | Labridae | Pseudocoris bleekeri | native | Philippines wrasse | |
| Eupercaria/misc | Labridae | Pseudocoris yamashiroi | native | Redspot wrasse | |
| Gobiiformes | Gobiidae | Pseudogobius masago | native | Masago snubnose goby | |
| Gobiiformes | Gobiidae | Pseudogobius poicilosoma | native | Northern fatnose goby | |
| Perciformes/Serranoidei | Grammistidae | Pseudogramma polyacantha | native | Honeycomb podge | |
| Eupercaria/misc | Labridae | Pseudojuloides severnsi | native | Severns' wrasse | |
| Eupercaria/misc | Labridae | Pseudojuloides splendens | native | Splendid pencil wrasse | |
| Ovalentaria/misc | Pseudochromidae | Pseudoplesiops annae | native | Anna's dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudoplesiops rosae | native | Rose Island basslet | |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus arsius | native | Largetooth flounder | |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus oligodon | native | Roughscale flounder | |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus pentophthalmus | native | Fivespot flounder | |
| Gobiiformes | Gobiidae | Psilogobius prolatus | native | Longjaw shrimpgoby | |
| Gobiiformes | Microdesmidae | Ptereleotris evides | native | Blackfin dartfish | Sakurai-kuroyuri-haze |
| Gobiiformes | Microdesmidae | Ptereleotris grammica | native | Lined dartfish | |
| Gobiiformes | Microdesmidae | Ptereleotris heteroptera | native | Blacktail goby | |
| Gobiiformes | Microdesmidae | Ptereleotris microlepis | native | Blue gudgeon | |
| Gobiiformes | Microdesmidae | Ptereleotris monoptera | native | Lyre-tail dart-goby | |
| Gobiiformes | Microdesmidae | Ptereleotris zebra | native | Chinese zebra goby | |
| Eupercaria/misc | Caesionidae | Pterocaesio digramma | native | Double-lined fusilier | |
| Eupercaria/misc | Caesionidae | Pterocaesio marri | native | Marr's fusilier | |
| Eupercaria/misc | Caesionidae | Pterocaesio pisang | native | Banana fusilier | |
| Eupercaria/misc | Caesionidae | Pterocaesio tile | native | Dark-banded fusilier | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois paucispinula | native | ||
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois radiata | native | Radial firefish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois volitans | native | Red lionfish | |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla ryukyuensis | native | Ryukyu gurnard | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis acares | native | Midget chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis atripes | native | Dark-fin chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis leucurus | native | Whitetail chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis ovatiformis | native | Ovate chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis pacifica | native | Pacific bronze Chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis retrofasciatus | native | Black-bar chromis | |
| Acanthuriformes | Pomacanthidae | Pygoplites diacanthus | native | Regal angelfish | |
| Perciformes/Serranoidei | Anthiadidae | Pyronotanthias flavoguttatus | native | Yellow-spotted anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pyronotanthias lori | native | Lori's anthias | |
| Eupercaria/misc | Lutjanidae | Randallichthys filamentosus | native | Randall's snapper | |
| Scombriformes | Scombridae | Rastrelliger kanagurta | native | Indian mackerel | |
| Scombriformes | Gempylidae | Rexea bengalensis | native | Bengal escolar | |
| Scombriformes | Gempylidae | Rexea nakamurai | native | Nakamura's escolar | |
| Scombriformes | Gempylidae | Rexea prometheoides | native | Royal escolar | |
| Kurtiformes | Apogonidae | Rhabdamia gracilis | native | Luminous cardinalfish | |
| Blenniiformes | Blenniidae | Rhabdoblennius nitidus | native | Barred-chin blenny | |
| Orectolobiformes | Rhincodontidae | Rhincodon typus | native | Whale shark | |
| Tetraodontiformes | Balistidae | Rhinecanthus abyssus | native | ||
| Tetraodontiformes | Balistidae | Rhinecanthus rectangulus | native | Wedge-tail triggerfish | |
| Anguilliformes | Muraenidae | Rhinomuraena quaesita | native | Ribbon moray | |
| Myliobatiformes | Rhinopteridae | Rhinoptera javanica | native | Flapnose ray | |
| Myliobatiformes | Rhinopteridae | Rhinoptera jayakari | native | Oman cownose ray | |
| Pleuronectiformes | Soleidae | Rhinosolea microlepidota | native | ||
| Acanthuriformes | Chaetodontidae | Roa modesta | native | Brown-banded butterflyfish | |
| Perciformes/Scorpaenoidei | Platycephalidae | Rogadius patriciae | native | Black-banded flathead | |
| Tetraodontiformes | Monacanthidae | Rudarius excelsus | native | Diamond leatherjacket | |
| Scombriformes | Gempylidae | Ruvettus pretiosus | native | Oilfish | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Ryukyupercis gushikeni | native | Rosy grubfish | |
| Blenniiformes | Blenniidae | Salarias fasciatus | native | Jewelled blenny | |
| Blenniiformes | Blenniidae | Salarias luctuosus | native | ||
| Blenniiformes | Blenniidae | Salarias segmentatus | native | Segmented blenny | |
| Blenniiformes | Blenniidae | Salarias sinuosus | native | Fringelip blenny | |
| Perciformes/Serranoidei | Epinephelidae | Saloptia powelli | native | Golden grouper | |
| Scombriformes | Scombridae | Sarda orientalis | native | Striped bonito | |
| Clupeiformes | Dorosomatidae | Sardinella alcyone | native | Blueback Sardinella | |
| Clupeiformes | Dorosomatidae | Sardinella electra | native | Island Sardinella | |
| Clupeiformes | Dorosomatidae | Sardinella lemuru | native | Bali sardinella | |
| Clupeiformes | Dorosomatidae | Sardinella zunasi | native | Japanese sardinella | |
| Holocentriformes | Holocentridae | Sargocentron caudimaculatum | native | Silverspot squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron diadema | native | Crown squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron dorsomaculatum | native | Spotfin squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron ensifer | native | Yellow-striped squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron ittodai | native | Samurai squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron melanospilos | native | Blackblotch squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron microstoma | native | Smallmouth squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron praslin | native | Dark-striped squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron punctatissimum | native | Speckled squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron spiniferum | native | Sabre squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron spinosissimum | native | North Pacific squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron tiere | native | Blue lined squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron tiereoides | native | Pink squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron violaceum | native | Violet squirrelfish | |
| Aulopiformes | Synodontidae | Saurida gracilis | native | Gracile lizardfish | |
| Aulopiformes | Synodontidae | Saurida nebulosa | native | Clouded lizardfish | |
| Gobiiformes | Oxudercidae | Scartelaos histophorus | native | Walking goby | |
| Eupercaria/misc | Scaridae | Scarus altipinnis | native | Filament-finned parrotfish | |
| Eupercaria/misc | Scaridae | Scarus chameleon | native | Chameleon parrotfish | |
| Eupercaria/misc | Scaridae | Scarus dimidiatus | native | Yellowbarred parrotfish | |
| Eupercaria/misc | Scaridae | Scarus festivus | native | Festive parrotfish | |
| Eupercaria/misc | Scaridae | Scarus forsteni | native | Forsten's parrotfish | |
| Eupercaria/misc | Scaridae | Scarus fuscocaudalis | native | Darktail parrotfish | |
| Eupercaria/misc | Scaridae | Scarus globiceps | native | Globehead parrotfish | |
| Eupercaria/misc | Scaridae | Scarus hypselopterus | native | Yellow-tail parrotfish | |
| Eupercaria/misc | Scaridae | Scarus niger | native | Dusky parrotfish | |
| Eupercaria/misc | Scaridae | Scarus oviceps | native | Dark capped parrotfish | |
| Eupercaria/misc | Scaridae | Scarus ovifrons | native | Knobsnout parrotfish | |
| Eupercaria/misc | Scaridae | Scarus prasiognathos | native | Singapore parrotfish | |
| Eupercaria/misc | Scaridae | Scarus quoyi | native | Quoy's parrotfish | |
| Eupercaria/misc | Scaridae | Scarus rivulatus | native | Rivulated parrotfish | |
| Eupercaria/misc | Scaridae | Scarus rubroviolaceus | native | Ember parrotfish | |
| Eupercaria/misc | Scaridae | Scarus schlegeli | native | Yellowband parrotfish | |
| Eupercaria/misc | Scaridae | Scarus spinus | native | Greensnout parrotfish | |
| Eupercaria/misc | Scaridae | Scarus xanthopleura | native | Red parrotfish | |
| Acanthuriformes | Scatophagidae | Scatophagus argus | native | Spotted scat | |
| Gobiiformes | Schindleriidae | Schindleria praematura | native | Schindler's fish | |
| Anguilliformes | Ophichthidae | Scolecenchelys gymnota | native | Indo-Pacific slender worm-eel | |
| Anguilliformes | Ophichthidae | Scolecenchelys macroptera | native | Narrow worm eel | |
| Eupercaria/misc | Nemipteridae | Scolopsis affinis | native | Peters' monocle bream | |
| Eupercaria/misc | Nemipteridae | Scolopsis bilineata | native | Two-lined monocle bream | |
| Eupercaria/misc | Nemipteridae | Scolopsis ciliata | native | Saw-jawed monocle bream | |
| Eupercaria/misc | Nemipteridae | Scolopsis lineata | native | Striped monocle bream | |
| Eupercaria/misc | Nemipteridae | Scolopsis monogramma | native | Monogrammed monocle bream | |
| Eupercaria/misc | Nemipteridae | Scolopsis vosmeri | native | Whitecheek monocle bream | |
| Scombriformes | Scombridae | Scomber australasicus | native | Blue mackerel | |
| Carangiformes | Carangidae | Scomberoides commersonnianus | native | Talang queenfish | |
| Carangiformes | Carangidae | Scomberoides lysan | native | Doublespotted queenfish | |
| Carangiformes | Carangidae | Scomberoides tol | native | Needlescaled queenfish | |
| Scombriformes | Scombridae | Scomberomorus commerson | native | Narrow-barred Spanish mackerel | |
| Acropomatiformes | Scombropidae | Scombrops boops | native | Gnomefish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes albaiensis | native | Longfingered scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes hirsutus | native | Hairy scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes kelloggi | native | Kellogg's scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes minor | native | Minor scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes parvipinnis | native | Lowfin scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes quadrispinosus | native | Fourspine scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis diabolus | native | False stonefish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis macrochir | native | Flasher scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis papuensis | native | Papuan scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis possi | native | Poss's scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis vittapinna | native | Bandfin scorpionfish | |
| Anguilliformes | Muraenidae | Scuticaria okinawae | native | Shorttailed snake moray | |
| Anguilliformes | Muraenidae | Scuticaria tigrina | native | Tiger reef-eel | |
| Carcharhiniformes | Scyliorhinidae | Scyliorhinus torazame | native | Cloudy catshark | |
| Carangiformes | Carangidae | Scyris indica | native | Indian threadfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes cyanostigma | native | Yellowspotted scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes fowleri | native | Pigmy scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes mauritiana | native | Spineblotch scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes strongia | native | Barchin scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes tinkhami | native | Darkspotted scorpionfish | |
| Carangiformes | Carangidae | Selar boops | native | Oxeye scad | |
| Carangiformes | Carangidae | Selar crumenophthalmus | native | Bigeye scad | |
| Carangiformes | Carangidae | Selaroides leptolepis | native | Yellowstripe scad | |
| Carangiformes | Carangidae | Seriola rivoliana | native | Longfin yellowtail | |
| Perciformes/Serranoidei | Anthiadidae | Serranocirrhitus latus | native | Hawkfish anthias | |
| Acanthuriformes | Siganidae | Siganus argenteus | native | Streamlined spinefoot | |
| Acanthuriformes | Siganidae | Siganus canaliculatus | native | White-spotted spinefoot | |
| Acanthuriformes | Siganidae | Siganus corallinus | native | Blue-spotted spinefoot | |
| Acanthuriformes | Siganidae | Siganus fuscescens | native | Mottled spinefoot | |
| Acanthuriformes | Siganidae | Siganus guttatus | native | Orange-spotted spinefoot | |
| Acanthuriformes | Siganidae | Siganus puellus | native | Masked spinefoot | |
| Acanthuriformes | Siganidae | Siganus punctatissimus | native | Peppered spinefoot | |
| Acanthuriformes | Siganidae | Siganus punctatus | native | Goldspotted spinefoot | |
| Acanthuriformes | Siganidae | Siganus spinus | native | Little spinefoot | |
| Acanthuriformes | Siganidae | Siganus unimaculatus | native | Blotched foxface | |
| Acanthuriformes | Siganidae | Siganus vermiculatus | native | Vermiculated spinefoot | |
| Acanthuriformes | Siganidae | Siganus virgatus | native | Barhead spinefoot | |
| Gobiiformes | Gobiidae | Silhouettea insinuans | native | Phantom goby | |
| Eupercaria/misc | Sillaginidae | Sillago aeolus | native | Oriental sillago | |
| Eupercaria/misc | Sillaginidae | Sillago sihama | native | Silver sillago | |
| Rajiformes | Anacanthobatidae | Sinobatis borneensis | native | Borneo leg skate | |
| Kurtiformes | Apogonidae | Siphamia majimai | native | Striped siphonfish | |
| Kurtiformes | Apogonidae | Siphamia tubifer | native | Tubifer cardinalfish | |
| Perciformes/Scorpaenoidei | Tetrarogidae | Snyderina yamanokami | native | ||
| Pleuronectiformes | Soleidae | Soleichthys heterorhinos | native | Black-tip sole | |
| Kurtiformes | Apogonidae | Sphaeramia nematoptera | native | Pajama cardinalfish | |
| Kurtiformes | Apogonidae | Sphaeramia orbicularis | native | Orbiculate cardinalfish | |
| Carangaria/misc | Sphyraenidae | Sphyraena acutipinnis | native | Sharpfin barracuda | |
| Carangaria/misc | Sphyraenidae | Sphyraena flavicauda | native | Yellowtail barracuda | |
| Carangaria/misc | Sphyraenidae | Sphyraena forsteri | native | Bigeye barracuda | |
| Carangaria/misc | Sphyraenidae | Sphyraena jello | native | Pickhandle barracuda | |
| Carangaria/misc | Sphyraenidae | Sphyraena obtusata | native | Obtuse barracuda | |
| Carangaria/misc | Sphyraenidae | Sphyraena qenie | native | Blackfin barracuda | |
| Carcharhiniformes | Sphyrnidae | Sphyrna lewini | native | Scalloped hammerhead | |
| Carcharhiniformes | Sphyrnidae | Sphyrna mokarran | native | Great hammerhead | |
| Clupeiformes | Spratelloididae | Spratelloides delicatulus | native | Delicate round herring | |
| Clupeiformes | Spratelloididae | Spratelloides gracilis | native | Silver-stripe round herring | |
| Blenniiformes | Clinidae | Springeratus xanthosoma | native | Indonesia weedfish | |
| Squaliformes | Squalidae | Squalus brevirostris | native | ||
| Squaliformes | Squalidae | Squalus japonicus | native | Japanese spurdog | |
| Squaliformes | Squalidae | Squalus megalops | native | Shortnose spurdog | |
| Squaliformes | Squalidae | Squalus mitsukurii | native | Shortspine spurdog | |
| Squatiniformes | Squatinidae | Squatina japonica | native | Japanese angelshark | |
| Squatiniformes | Squatinidae | Squatina nebulosa | native | Clouded angelshark | |
| Blenniiformes | Blenniidae | Stanulus talboti | native | Talbot's blenny | |
| Ovalentaria/misc | Pomacentridae | Stegastes albifasciatus | native | Whitebar gregory | |
| Ovalentaria/misc | Pomacentridae | Stegastes lacrymatus | native | Whitespotted devil | |
| Ovalentaria/misc | Pomacentridae | Stegastes nigricans | native | Dusky farmerfish | |
| Ovalentaria/misc | Pomacentridae | Stegastes punctatus | native | Blunt snout gregory | |
| Anguilliformes | Serrivomeridae | Stemonidium hypomelas | native | Black serrivomerid eel | |
| Gobiiformes | Gobiidae | Stonogobiops nematodes | native | Filament-finned prawn-goby | |
| Gobiiformes | Gobiidae | Stonogobiops xanthorhinicus | native | Yellownose prawn-goby | |
| Gobiiformes | Gobiidae | Stonogobiops yasha | native | Orange-striped shrimpgoby | |
| Beloniformes | Belonidae | Strongylura incisa | native | Reef needlefish | |
| Anguilliformes | Muraenidae | Strophidon sathete | native | Slender giant moray | |
| Tetraodontiformes | Balistidae | Sufflamen fraenatum | native | Masked triggerfish | |
| Perciformes/Scorpaenoidei | Platycephalidae | Sunagocia arenicola | native | Broadhead flathead | |
| Perciformes/Scorpaenoidei | Platycephalidae | Sunagocia otaitensis | native | Fringelip flathead | |
| Eupercaria/misc | Lutjanidae | Symphorichthys spilurus | native | Sailfin snapper | |
| Eupercaria/misc | Lutjanidae | Symphorus nematophorus | native | Chinamanfish | |
| Pleuronectiformes | Cynoglossidae | Symphurus hondoensis | native | ||
| Perciformes/Scorpaenoidei | Synanceiidae | Synanceia verrucosa | native | Stonefish | |
| Callionymiformes | Callionymidae | Synchiropus morrisoni | native | Morrison's dragonet | |
| Callionymiformes | Callionymidae | Synchiropus moyeri | native | Moyer's dragonet | |
| Callionymiformes | Callionymidae | Synchiropus ocellatus | native | Ocellated dragonet | |
| Callionymiformes | Callionymidae | Synchiropus splendidus | native | Mandarinfish | |
| Syngnathiformes | Syngnathidae | Syngnathus schlegeli | native | Seaweed pipefish | |
| Aulopiformes | Synodontidae | Synodus binotatus | native | Two-spot lizard fish | |
| Aulopiformes | Synodontidae | Synodus dermatogenys | native | Sand lizardfish | |
| Aulopiformes | Synodontidae | Synodus rubromarmoratus | native | Redmarbled lizardfish | |
| Aulopiformes | Synodontidae | Synodus variegatus | native | Variegated lizardfish | |
| Kurtiformes | Apogonidae | Taeniamia biguttata | native | Twinspot cardinalfish | |
| Kurtiformes | Apogonidae | Taeniamia fucata | native | Orangelined cardinalfish | |
| Kurtiformes | Apogonidae | Taeniamia zosterophora | native | Blackbelted cardinalfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Taenianotus triacanthus | native | Leaf scorpionfish | |
| Gobiiformes | Gobiidae | Taenioides limicola | native | ||
| Tetraodontiformes | Tetraodontidae | Takifugu niphobles | native | ||
| Tetraodontiformes | Tetraodontidae | Takifugu poecilonotus | native | ||
| Alepocephaliformes | Alepocephalidae | Talismania antillarum | native | Antillean smooth-head | |
| Alepocephaliformes | Alepocephalidae | Talismania filamentosa | native | ||
| Alepocephaliformes | Alepocephalidae | Talismania okinawensis | endemic | ||
| Scombriformes | Trichiuridae | Tentoriceps cristatus | native | Crested hairtail | |
| Centrarchiformes | Terapontidae | Terapon jarbua | native | Jarbua terapon | |
| Centrarchiformes | Terapontidae | Terapon theraps | native | Largescaled terapon | |
| Carangiformes | Istiophoridae | Tetrapturus angustirostris | native | Shortbill spearfish | |
| Perciformes/Scorpaenoidei | Tetrarogidae | Tetraroge barbata | native | Bearded roguefish | |
| Perciformes/Scorpaenoidei | Tetrarogidae | Tetraroge nigra | native | ||
| Eupercaria/misc | Labridae | Thalassoma lunare | native | Moon wrasse | |
| Eupercaria/misc | Labridae | Thalassoma purpureum | native | Surge wrasse | |
| Eupercaria/misc | Labridae | Thalassoma quinquevittatum | native | Fivestripe wrasse | |
| Eupercaria/misc | Labridae | Thalassoma trilobatum | native | Christmas wrasse | |
| Scombriformes | Scombridae | Thunnus alalunga | native | Albacore | |
| Scombriformes | Scombridae | Thunnus albacares | native | Yellowfin tuna | |
| Scombriformes | Scombridae | Thunnus obesus | native | Bigeye tuna | |
| Scombriformes | Scombridae | Thunnus orientalis | native | Pacific bluefin tuna | |
| Scombriformes | Gempylidae | Thyrsitoides marleyi | native | Black snoek | |
| Perciformes/Scorpaenoidei | Platycephalidae | Thysanophrys chiltonae | native | Longsnout flathead | |
| Gobiiformes | Gobiidae | Tomiyamichthys emilyae | native | Emily’s shrimpgoby | |
| Gobiiformes | Gobiidae | Tomiyamichthys lanceolatus | native | Lanceolate shrimpgoby | |
| Gobiiformes | Gobiidae | Tomiyamichthys oni | native | Monster shrimpgoby | |
| Tetraodontiformes | Tetraodontidae | Torquigener albomaculosus | native | White-spotted pufferfish | |
| Carangaria/misc | Toxotidae | Toxotes jaculatrix | native | Banded archerfish | |
| Carangiformes | Carangidae | Trachinotus baillonii | native | Small spotted dart | |
| Carangiformes | Carangidae | Trachinotus blochii | native | Snubnose pompano | |
| Carangiformes | Carangidae | Trachurus japonicus | native | Japanese jack mackerel | |
| Carcharhiniformes | Carcharhinidae | Triaenodon obesus | native | Whitetip reef shark | |
| Scombriformes | Trichiuridae | Trichiurus lepturus | native | Largehead hairtail | |
| Gobiiformes | Trichonotidae | Trichonotus elegans | native | Long-rayed sand-diver | |
| Gobiiformes | Gobiidae | Trimma caesiura | native | Caesiura pygmygoby | |
| Gobiiformes | Gobiidae | Trimma caudipunctatum | native | Spot-tailed pygmygoby | |
| Gobiiformes | Gobiidae | Trimma caudomaculatum | native | Blotch-tailed pygmygoby | |
| Gobiiformes | Gobiidae | Trimma emeryi | native | Emery's pygmygoby | |
| Gobiiformes | Gobiidae | Trimma flavatrum | native | Wasp pygmygoby | |
| Gobiiformes | Gobiidae | Trimma hayashii | native | Four-eye pygmygoby | |
| Gobiiformes | Gobiidae | Trimma kudoi | native | Kudo's pygmygoby | |
| Gobiiformes | Gobiidae | Trimma marinae | native | Princess pygmygoby | |
| Gobiiformes | Gobiidae | Trimma naudei | native | Naude's pygmygoby | |
| Gobiiformes | Gobiidae | Trimma nomurai | native | Lilac pygmygoby | |
| Gobiiformes | Gobiidae | Trimma okinawae | native | Orange-red pygmygoby | |
| Gobiiformes | Gobiidae | Trimma sheppardi | native | Sheppard's pygmygoby | |
| Gobiiformes | Gobiidae | Trimma yanoi | native | Pudgy pygmygoby | |
| Gobiiformes | Gobiidae | Trimma yoshinoi | native | Yoshino's pygmygoby | |
| Gobiiformes | Gobiidae | Tryssogobius colini | native | Colin's fairygoby | |
| Gobiiformes | Gobiidae | Tryssogobius nigrolineatus | native | Deepreef fairygoby | |
| Gobiiformes | Gobiidae | Tryssogobius sarah | native | Sarah's fairygoby | |
| Carangiformes | Carangidae | Turrum coeruleopinnatum | native | Coastal trevally | |
| Carangiformes | Carangidae | Turrum fulvoguttatum | native | Yellowspotted trevally | |
| Carangiformes | Carangidae | Turrum gymnostethus | native | Bludger | |
| Blenniiformes | Tripterygiidae | Ucla xenogrammus | native | Largemouth triplefin | |
| Mulliformes | Mullidae | Upeneus moluccensis | native | Goldband goatfish | |
| Mulliformes | Mullidae | Upeneus subvittatus | native | Deep-water goatfish | |
| Mulliformes | Mullidae | Upeneus sulphureus | native | Sulphur goatfish | |
| Mulliformes | Mullidae | Upeneus taeniopterus | native | Finstripe goatfish | |
| Mulliformes | Mullidae | Upeneus tragula | native | Freckled goatfish | |
| Mulliformes | Mullidae | Upeneus vittatus | native | Yellowstriped goatfish | |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus bicinctus | native | Marbled stargazer | |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus japonicus | native | ||
| Carangiformes | Carangidae | Uraspis uraspis | native | Whitemouth jack | |
| Syngnathiformes | Syngnathidae | Urocampus nanus | native | Barbed pipefish | |
| Anguilliformes | Muraenidae | Uropterygius concolor | native | Unicolor snake moray | |
| Anguilliformes | Muraenidae | Uropterygius marmoratus | native | Marbled reef-eel | |
| Anguilliformes | Muraenidae | Uropterygius micropterus | native | Tidepool snake moray | |
| Anguilliformes | Muraenidae | Uropterygius nagoensis | native | Nago snakemoray | |
| Gobiiformes | Gobiidae | Valenciennea bella | native | Bella goby | |
| Gobiiformes | Gobiidae | Valenciennea longipinnis | native | Long-finned goby | |
| Gobiiformes | Gobiidae | Valenciennea muralis | native | Mural goby | |
| Gobiiformes | Gobiidae | Valenciennea parva | native | Parva goby | |
| Gobiiformes | Gobiidae | Valenciennea randalli | native | Greenband goby | |
| Gobiiformes | Gobiidae | Valenciennea sexguttata | native | Sixspot goby | |
| Gobiiformes | Gobiidae | Valenciennea strigata | native | Blueband goby | |
| Gobiiformes | Gobiidae | Valenciennea yanoi | native | ||
| Gobiiformes | Gobiidae | Vanderhorstia ambanoro | native | Ambanoro prawn-goby | |
| Gobiiformes | Gobiidae | Vanderhorstia dorsomacula | native | Dorsalspot shrimpgoby | |
| Gobiiformes | Gobiidae | Vanderhorstia fulvopelvis | native | ||
| Gobiiformes | Gobiidae | Vanderhorstia ornatissima | native | Ornate prawn-goby | |
| Gobiiformes | Gobiidae | Vanderhorstia papilio | native | Butterfly shrimpgoby | |
| Gobiiformes | Gobiidae | Vanderhorstia phaeosticta | native | Yellowfoot shrimpgoby | |
| Perciformes/Serranoidei | Epinephelidae | Variola albimarginata | native | White-edged lyretail | |
| Perciformes/Serranoidei | Epinephelidae | Variola louti | native | Yellow-edged lyretail | |
| Gadiformes | Macrouridae | Ventrifossa garmani | native | Sagami grenadier | |
| Gadiformes | Macrouridae | Ventrifossa macroptera | native | Palau grenadier | |
| Gadiformes | Macrouridae | Ventrifossa nigrodorsalis | native | Spinaker grenadier | |
| Pleuronectiformes | Pleuronectidae | Verasper variegatus | native | Spotted halibut | |
| Acropomatiformes | Malakichthyidae | Verilus pacificus | native | ||
| Kurtiformes | Apogonidae | Verulux cypselurus | native | Swallowtail cardinalfish | |
| Stomiiformes | Phosichthyidae | Vinciguerria attenuata | native | Slender lightfish | |
| Eupercaria/misc | Lethrinidae | Wattsia mossambica | native | Mozambique large-eye bream | |
| Eupercaria/misc | Labridae | Wetmorella nigropinnata | native | Sharpnose wrasse | |
| Tetraodontiformes | Balistidae | Xanthichthys auromarginatus | native | Gilded triggerfish | |
| Tetraodontiformes | Balistidae | Xanthichthys caeruleolineatus | native | Outrigger triggerfish | |
| Tetraodontiformes | Balistidae | Xanthichthys lineopunctatus | native | Striped triggerfish | |
| Tetraodontiformes | Balistidae | Xanthichthys mento | native | Redtail triggerfish | |
| Gobiiformes | Xenisthmidae | Xenisthmus clarus | native | Clear wriggler | |
| Gobiiformes | Xenisthmidae | Xenisthmus polyzonatus | native | Bullseye wriggler | |
| Eupercaria/misc | Labridae | Xenojulis margaritacea | native | Finspot wrasse | |
| Carangiformes | Xiphiidae | Xiphias gladius | native | Swordfish | |
| Squaliformes | Somniosidae | Zameus squamulosus | native | Velvet dogfish | |
| Acanthuriformes | Acanthuridae | Zebrasoma flavescens | native | Yellow tang | |
| Acanthuriformes | Acanthuridae | Zebrasoma scopas | native | Twotone tang | |
| Acanthuriformes | Acanthuridae | Zebrasoma velifer | native | Sailfin tang | |
| Pleuronectiformes | Soleidae | Zebrias japonica | native | Wavyband sole | |
| Beloniformes | Zenarchopteridae | Zenarchopterus dunckeri | native | Duncker's river garfish | |
| Kurtiformes | Apogonidae | Zoramia fragilis | native | Fragile cardinalfish | |
| Kurtiformes | Apogonidae | Zoramia gilberti | native | Gilbert's cardinalfish | |
| Kurtiformes | Apogonidae | Zoramia leptacanthus | native | Threadfin cardinalfish |