| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Australian | Zoogeographic realm | native | 2847 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Malacca Strait | Sea/Bay/Gulf | native | 121464 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Oriental | Zoogeographic realm | native | 4833 |
| Pacific Ocean | Sea/Bay/Gulf | native | 48497 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45161 |
| Sikao Creek | River (basin) | native | 52823 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Taal Lake | Lake | native | 12165 |
| West Philippine Sea | Sea/Bay/Gulf | native | 48613 |