| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Davao Gulf | Sea/Bay/Gulf | questionable | 45419 |
| Indian Ocean | Sea/Bay/Gulf | native | 1921 |
| Lagonoy Gulf | Sea/Bay/Gulf | questionable | 43283 |
| Lingayen Gulf | Sea/Bay/Gulf | questionable | 5399 |
| Panay Gulf | Sea/Bay/Gulf | questionable | 42831 |
| Ragay Gulf | Sea/Bay/Gulf | questionable | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| South China Sea | Sea/Bay/Gulf | questionable | 45419 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | questionable | 45419 |
| Tubbataha Reefs | Sea/Bay/Gulf | questionable | 53416 |