| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 2295 |
| Andaman Sea | Sea/Bay/Gulf | native | 5736 |
| Arabian Sea | Sea/Bay/Gulf | native | 2295 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Chiku River | River (basin) | native | 36073 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2295 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 2295 |
| Gulf of Aden | Sea/Bay/Gulf | native | 2295 |
| Gulf of Oman | Sea/Bay/Gulf | native | 2295 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 2295 |
| Indian Ocean | Sea/Bay/Gulf | native | 2295 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2295 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104679 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2295 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 92948 |
| Ragay Gulf | Sea/Bay/Gulf | native | 38601 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| Sogod Bay | Sea/Bay/Gulf | native | 31411 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 2295 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 94637 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 10558 |
| Ulugan Bay | Sea/Bay/Gulf | native | 43468 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115274 |
| Yellow Sea | Sea/Bay/Gulf | native | 2295 |