| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 90102 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Erhjen River | River (basin) | native | 36073 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Indian Ocean | Sea/Bay/Gulf | native | 2136 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2136 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2136 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2136 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2136 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Shiliao River | River (basin) | native | 36073 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Yellow Sea | Sea/Bay/Gulf | native | 2136 |