| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| Bonaparte Coast | Sea/Bay/Gulf | native | 75154 |
| Central and Southern Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Chiku River | River (basin) | native | 36073 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erhjen River | River (basin) | native | 36073 |
| Indian Ocean | Sea/Bay/Gulf | native | 7050 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Mekong | River (basin) | native | 12693 |
| Oriental | Zoogeographic realm | endemic | 35840 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1479 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45674 |
| 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 |
| Tanshui River | River (basin) | native | 36073 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tsengwen River | River (basin) | native | 36073 |