| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Australian | Zoogeographic realm | native | 7050 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Naujan Lake | Lake | native | 13446 |
| Oriental | Zoogeographic realm | native | 280 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7300 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Palearctic | Zoogeographic realm | native | 41184 |
| Red Sea | Sea/Bay/Gulf | misidentification | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Shihtsao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Taal Lake | Lake | native | 12165 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |