| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7247 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7247 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Ulugan Bay | Sea/Bay/Gulf | native | 43468 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107853 |