| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 2295 |
| Andaman Sea | Sea/Bay/Gulf | native | 2295 |
| Arabian Sea | Sea/Bay/Gulf | native | 2295 |
| Bay of Bengal | Sea/Bay/Gulf | native | 2295 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2295 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 2295 |
| Gulf of Aden | Sea/Bay/Gulf | native | 2295 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Indian Ocean | Sea/Bay/Gulf | native | 2295 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2295 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 2295 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 68980 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2295 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2295 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2295 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 2295 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 2295 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |
| West Philippine Sea | Sea/Bay/Gulf | native | 5399 |
| Yellow Sea | Sea/Bay/Gulf | native | 2295 |