| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 12711 |
| South China Sea | Sea/Bay/Gulf | native | 12711 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| West Philippine Sea | Sea/Bay/Gulf | native | 48613 |
| Yellow Sea | Sea/Bay/Gulf | native | 12711 |