| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 188 |
| Andaman Sea | Sea/Bay/Gulf | native | 188 |
| Arabian Sea | Sea/Bay/Gulf | native | 188 |
| Australian | Zoogeographic realm | native | 7300 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| Canal des Pangalanes | River (basin) | native | 26236 |
| Ethiopian | Zoogeographic realm | native | 3509 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Gulf of Aden | Sea/Bay/Gulf | native | 188 |
| Gulf of Oman | Sea/Bay/Gulf | native | 188 |
| Indian Ocean | Sea/Bay/Gulf | native | 188 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| North Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Oriental | Zoogeographic realm | native | 188 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7300 |
| Pangani | River (basin) | native | 188 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Rufiji | River (basin) | native | 93960 |
| Ruvu | River (basin) | native | 93960 |
| Sabaki | River (basin) | native | 30558 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 188 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 188 |
| Tana | River (basin) | native | 52331 |
| Zanzibar | River (basin) | native | 93960 |