| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bismarck Sea | Sea/Bay/Gulf | native | 130185 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Halmahera | Sea/Bay/Gulf | native | 649 |
| Indian Ocean | Sea/Bay/Gulf | native | 130185 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lesser Sunda | Sea/Bay/Gulf | native | 130185 |
| Pacific Ocean | Sea/Bay/Gulf | native | 130185 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 1602 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130185 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |