| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Andaman Sea | Sea/Bay/Gulf | native | 54393 |
| Cargados Carajos Shoals | Sea/Bay/Gulf | native | 54393 |
| Gulf of Aden | Sea/Bay/Gulf | native | 54393 |
| Gulf of Aqaba | Sea/Bay/Gulf | native | 54393 |
| Gulf of Oman | Sea/Bay/Gulf | native | 11441 |
| Indian Ocean | Sea/Bay/Gulf | native | 3470 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 30874 |
| Pacific Ocean | Sea/Bay/Gulf | native | 30874 |
| Persian Gulf | Sea/Bay/Gulf | native | 68964 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 12484 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107853 |