| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Australian | Zoogeographic realm | native | 13299 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1602 |
| Ethiopian | Zoogeographic realm | native | 3412 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Gulf of Oman | Sea/Bay/Gulf | native | 11441 |
| Indian Ocean | Sea/Bay/Gulf | native | 3412 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 3412 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Oriental | Zoogeographic realm | native | 87596 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1602 |
| Palearctic | Zoogeographic realm | native | 1602 |
| Persian Gulf | Sea/Bay/Gulf | native | 1602 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| Sikao Creek | River (basin) | native | 52823 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Tsengwen River | River (basin) | native | 36073 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115274 |