| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 7247 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7247 |
| North Australian Shelf | Sea/Bay/Gulf | native | 7247 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7247 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107854 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |