| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chiku River | River (basin) | native | 36073 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2334 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 106380 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erhjen River | River (basin) | native | 36073 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Malalag Bay | Sea/Bay/Gulf | native | 106380 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2334 |
| 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 | 68964 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Ruerhmen River | River (basin) | native | 36073 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45161 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| Shark Bay | Sea/Bay/Gulf | native | 115321 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 7223 |
| Tañon Strait | Sea/Bay/Gulf | native | 11337 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Ulugan Bay | Sea/Bay/Gulf | native | 43468 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115321 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |