| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Australian | Zoogeographic realm | native | 5259 |
| Central and Southern Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Ethiopian | Zoogeographic realm | native | 5259 |
| Laguna de Bay | Lake | native | 13460 |
| Lake Lanao | Lake | introduced | 10888 |
| Lake Mainit | Lake | native | 4867 |
| Naujan Lake | Lake | native | 13446 |
| Oriental | Zoogeographic realm | native | 45255 |
| South China Sea | Sea/Bay/Gulf | native | 11915 |
| Taal Lake | Lake | native | 12165 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |