| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 168 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Bay of Bengal | Sea/Bay/Gulf | native | 168 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 168 |
| Indian Ocean | Sea/Bay/Gulf | native | 168 |
| Indonesian Sea | Sea/Bay/Gulf | native | 168 |
| 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 | 35686 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Ragay Gulf | Sea/Bay/Gulf | native | 38601 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Sogod Bay | Sea/Bay/Gulf | native | 31411 |
| 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 | 10558 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107093 |