| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bensbach River | River (basin) | native | 50786 |
| Chiku River | River (basin) | native | 36073 |
| Erhjen River | River (basin) | native | 36073 |
| Indian Ocean | Sea/Bay/Gulf | native | 4180 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Kaoping River | River (basin) | native | 36073 |
| Naujan Lake | Lake | native | 13446 |
| Oriental | Zoogeographic realm | native | 4833 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 4833 |
| Palearctic | Zoogeographic realm | native | 5193 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 94637 |
| Taal Lake | Lake | native | 12165 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tsengwen River | River (basin) | native | 36073 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43510 |
| Yun-gan | Sea/Bay/Gulf | native | 43515 |