| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bay of Bengal | Sea/Bay/Gulf | native | 42740 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 559 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 42740 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 128223 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 37603 |
| West Philippine Sea | Sea/Bay/Gulf | native | 5399 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |