| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Arnhem Coast to Gulf of Carpenteria | Sea/Bay/Gulf | native | 75154 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2334 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Exmouth to Broome | Sea/Bay/Gulf | native | 75154 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Manning-Hawkesbury | Sea/Bay/Gulf | native | 75154 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2334 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Ragay Gulf | Sea/Bay/Gulf | native | 48011 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 7401 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Torres Strait Northern Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |