| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indonesian Sea | Sea/Bay/Gulf | native | 9823 |
| Pacific Ocean | Sea/Bay/Gulf | native | 9823 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 42643 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |