| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Andaman Sea | Sea/Bay/Gulf | native | 5736 |
| Arabian Sea | Sea/Bay/Gulf | native | 3507 |
| Bay of Bengal | Sea/Bay/Gulf | native | 2115 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Ethiopian | Zoogeographic realm | native | 4335 |
| Euphrates and Tigris Delta | River (basin) | native | 115344 |
| Gulf of Aden | Sea/Bay/Gulf | native | 3507 |
| Gulf of Oman | Sea/Bay/Gulf | native | 3507 |
| Indian Ocean | Sea/Bay/Gulf | native | 4335 |
| Oriental | Zoogeographic realm | native | 5736 |
| Palearctic | Zoogeographic realm | native | 3507 |
| Persian Gulf | Sea/Bay/Gulf | native | 3507 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 3507 |
| Zambezi | River (basin) | native | 39194 |