| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 2295 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Indian Ocean | Sea/Bay/Gulf | native | 2295 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2295 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2295 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2295 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |