| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Chiku River | River (basin) | native | 36073 |
| Erhjen River | River (basin) | native | 36073 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 9790 |
| Indian Ocean | Sea/Bay/Gulf | native | 9790 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kaoping River | River (basin) | native | 36073 |
| Leyte Gulf | Sea/Bay/Gulf | native | 68980 |
| North Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7300 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45674 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46241 |
| Shark Bay | Sea/Bay/Gulf | native | 116003 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 94637 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 393 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |