| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Chiku River | River (basin) | native | 36073 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2295 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | questionable | 2295 |
| Insular Pacific-Hawaiian | Sea/Bay/Gulf | questionable | 583 |
| Kuroshio Current | Sea/Bay/Gulf | questionable | 2295 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| North Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Pacific Ocean | Sea/Bay/Gulf | native | 6390 |
| Palawan/North Borneo | Sea/Bay/Gulf | native | 121724 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 5193 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42419 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115274 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |