| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 45419 |
| East China Sea | Sea/Bay/Gulf | native | 37816 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48451 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Pacific Ocean | Sea/Bay/Gulf | native | 4868 |
| Palawan/North Borneo | Sea/Bay/Gulf | native | 121724 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 31075 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 37603 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |