| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 45255 |
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 4959 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East China Sea | Sea/Bay/Gulf | native | 11230 |
| Gulf of Oman | Sea/Bay/Gulf | native | 11441 |
| Honda Bay | Sea/Bay/Gulf | native | 71000 |
| Indian Ocean | Sea/Bay/Gulf | native | 3424 |
| Indonesian Sea | Sea/Bay/Gulf | native | 6567 |
| 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 |
| Manila Bay | Sea/Bay/Gulf | native | 30919 |
| North Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 4959 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 58457 |
| Ragay Gulf | Sea/Bay/Gulf | native | 38601 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45161 |
| 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 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2858 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Visayan Sea | Sea/Bay/Gulf | native | 3557 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |