| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 103843 |
| Spratly Islands | Sea/Bay/Gulf | native | 103843 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 37603 |