| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 7247 |
| Bay of Bengal | Sea/Bay/Gulf | native | 7247 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Davao Gulf | Sea/Bay/Gulf | native | 45419 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 7247 |
| Indian Ocean | Sea/Bay/Gulf | native | 7247 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7247 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 3132 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 3132 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3132 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 559 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107854 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |