| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Arabian Sea | Sea/Bay/Gulf | native | 1602 |
| Australian | Zoogeographic realm | native | 6192 |
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Breede | River (basin) | native | 7248 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 4959 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erhjen River | River (basin) | native | 36073 |
| Ethiopian | Zoogeographic realm | native | 4337 |
| Gulf of Aden | Sea/Bay/Gulf | native | 5450 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Madagascar river drainages and lakes | River (basin) | native | 56151 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Oriental | Zoogeographic realm | native | 12693 |
| Pacific Ocean | Sea/Bay/Gulf | native | 4959 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Persian Gulf | Sea/Bay/Gulf | native | 37588 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Sabaki | River (basin) | native | 30558 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46241 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 30558 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 1602 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |