| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Davao Gulf | Sea/Bay/Gulf | native | 106380 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Panguil Bay | Sea/Bay/Gulf | native | 47692 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| South China Sea | Sea/Bay/Gulf | native | 4868 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 35545 |
| Tahiti I. | Sea/Bay/Gulf | native | 4795 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 37603 |