| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 3287 |
| Andaman Sea | Sea/Bay/Gulf | native | 5736 |
| Arabian Sea | Sea/Bay/Gulf | native | 3287 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 3197 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Bay of Bengal | Sea/Bay/Gulf | native | 3287 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chang-hwa | Sea/Bay/Gulf | native | 43515 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 3287 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 3287 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erh-jen-shi | Sea/Bay/Gulf | native | 43515 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 3197 |
| Gulf of Aden | Sea/Bay/Gulf | native | 3287 |
| Gulf of Oman | Sea/Bay/Gulf | native | 3287 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 3287 |
| Honda Bay | Sea/Bay/Gulf | native | 71000 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 43515 |
| Hsin-chu | Sea/Bay/Gulf | native | 43515 |
| Indian Ocean | Sea/Bay/Gulf | native | 3197 |
| Indonesian Sea | Sea/Bay/Gulf | native | 3287 |
| Kaoping River | River (basin) | native | 36073 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| Milne Bay | Sea/Bay/Gulf | native | 41468 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 3287 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 3287 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 3287 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 43515 |
| Persian Gulf | Sea/Bay/Gulf | native | 3287 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46241 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 3287 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2858 |
| Tai-chung | Sea/Bay/Gulf | native | 43515 |
| Tanshui River | River (basin) | native | 36073 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Tsengwen River | River (basin) | native | 36073 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43510 |
| Verde Island Passage | Sea/Bay/Gulf | native | 82367 |
| Visayan Sea | Sea/Bay/Gulf | native | 110389 |
| Yellow Sea | Sea/Bay/Gulf | native | 3287 |