| Microscolex dubius (Fletcher, 1887) |
| Microscolex phosphoreus (Dugès, 1837) |
| Microscolex troyeri (Eisen, 1893) |
| Protozapotecia Jam, 1994 |
| Protozapotecia acaxetlensis Cervantes & Fragoso, 2018 |
| Protozapotecia aquilonalis James, 1993 |
| Protozapotecia australis James, 1993 |
| Protozapotecia koebeli Eisen, 1900 |
| Protozapotecia oyametlensis Cervantes & Fragoso, 2018 |
| Protozapotecia unamensis Fragoso, Rojas, Álvarez-Sánchez, Barajas, Martínez-Hurtado & Martínez-Rodríguez, 2019 |
| Zapotecia Eisen, 1900 |
| Zapotecia amecameca Eisen, 1900 |
| Zapotecia nova James, 1993 |