| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 4423 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 1602 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1602 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48451 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Polynesian Waters | Sea/Bay/Gulf | native | 5439 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 1602 |
| Tahiti I. | Sea/Bay/Gulf | native | 28618 |
| Tanshui River | River (basin) | native | 36073 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 37603 |
| Wan-li-tung | Sea/Bay/Gulf | native | 43514 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |