| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1602 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Gulf of Aden | Sea/Bay/Gulf | native | 5450 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Kuroshio Current | Sea/Bay/Gulf | native | 1602 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Milne Bay | Sea/Bay/Gulf | native | 41468 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Persian Gulf | Sea/Bay/Gulf | native | 68964 |
| Polynesian Waters | Sea/Bay/Gulf | native | 1602 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2858 |
| Taal Lake | Lake | native | 13446 |
| Tahiti Basins | River (basin) | native | 89972 |
| Tahiti I. | Sea/Bay/Gulf | native | 89972 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |