| Family | Genus | Species |
|---|---|---|
| Amphifilaceae | 0 | 3 |
| Amphitraemidae | 2 | 4 |
| Bicosoecidae | 2 | 9 |
| Blastocystidae | 1 | 323 |
| Cafeteriaceae | 3 | 36 |
| Labyrinthulaceae | 1 | 30 |
| Opalinidae | 4 | 23 |
| Placidiaceae | 6 | 13 |
| Proteromonadidae | 2 | 7 |
| Pseudophyllomitidae | 1 | 3 |
| Siluaniidae | 7 | 12 |
| Thraustochytriaceae | 15 | 620 |