| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5222 |
| Calamianes Islands | Sea/Bay/Gulf | questionable | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 5222 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5222 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 5222 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 5222 |
| Pacific Ocean | Sea/Bay/Gulf | native | 5222 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Tubbataha Reefs | Sea/Bay/Gulf | questionable | 57038 |