| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | questionable | 559 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 9710 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Leyte Gulf | Sea/Bay/Gulf | native | 68980 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 11298 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Yellow Sea | Sea/Bay/Gulf | native | 12711 |