| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 45255 |
| Chiku River | River (basin) | native | 36073 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Indian Ocean | Sea/Bay/Gulf | native | 559 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| North Australian Shelf | Sea/Bay/Gulf | native | 5978 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 5978 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 5978 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 5978 |
| Peng-hu Island | Sea/Bay/Gulf | native | 43515 |
| Ruerhmen River | River (basin) | native | 36073 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 31075 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Tsengwen River | River (basin) | native | 36073 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |