| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Banda Sea | Sea/Bay/Gulf | native | 96968 |
| Bonaparte Coast | Sea/Bay/Gulf | native | 96968 |
| Cape Howe | Sea/Bay/Gulf | native | 96968 |
| Coral Sea | Sea/Bay/Gulf | native | 96968 |
| Exmouth to Broome | Sea/Bay/Gulf | native | 96968 |
| Great Australian Bight | Sea/Bay/Gulf | native | 96968 |
| Houtman | Sea/Bay/Gulf | native | 96968 |
| Indian Ocean | Sea/Bay/Gulf | native | 96968 |
| Leeuwin | Sea/Bay/Gulf | native | 96968 |
| Lesser Sunda | Sea/Bay/Gulf | native | 96968 |
| Manning-Hawkesbury | Sea/Bay/Gulf | native | 96968 |
| Ningaloo | Sea/Bay/Gulf | native | 96968 |
| Northeast Sulawesi | Sea/Bay/Gulf | native | 96968 |
| Pacific Ocean | Sea/Bay/Gulf | native | 96968 |
| Shark Bay | Sea/Bay/Gulf | native | 96968 |
| Southern Java | Sea/Bay/Gulf | native | 96968 |
| Torres Strait Northern Great Barrier Reef | Sea/Bay/Gulf | native | 96968 |
| Tweed-Moreton | Sea/Bay/Gulf | native | 96968 |