| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1419 |
| Davao Gulf | Sea/Bay/Gulf | native | 106380 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 1419 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Indian Ocean | Sea/Bay/Gulf | native | 1419 |
| Indonesian Sea | Sea/Bay/Gulf | native | 1419 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1419 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1419 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 1419 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1419 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Polynesian Waters | Sea/Bay/Gulf | native | 1419 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45161 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| Sarangani Bay | Sea/Bay/Gulf | native | 106380 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Tahiti Basins | River (basin) | native | 12792 |
| Tañon Strait | Sea/Bay/Gulf | native | 11337 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Yellow Sea | Sea/Bay/Gulf | native | 1419 |