| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Chang-hwa | Sea/Bay/Gulf | native | 43515 |
| East China Sea | Sea/Bay/Gulf | native | 11230 |
| Erhjen River | River (basin) | native | 36073 |
| Kaoping River | River (basin) | native | 36073 |
| Mediterranean Sea | Sea/Bay/Gulf | questionable | 93672 |
| Neotropical | Zoogeographic realm | introduced | 559 |
| Oriental | Zoogeographic realm | introduced | 2682 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2682 |
| Palearctic | Zoogeographic realm | native | 9988 |
| Peng-hu Island | Sea/Bay/Gulf | native | 43515 |
| Ruerhmen River | River (basin) | native | 36073 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 2682 |
| Tai-chung | Sea/Bay/Gulf | native | 43515 |
| Tsengwen River | River (basin) | native | 36073 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43510 |