The group is split into two suborders, Holectypina and Pygasterina, on the basis of apical disc structure and periproct position. The suborder Pygasterina contains some of the most primitive known irregular echinoids.
Characters supporting the groupings in the cladogram shown above are as follows:
1. Genital plate 5 absent; periproct a large keyhole-shaped opening on the aboral surface.
2. Periproct positioned just above the ambitus, and separated from the apical disc by a series of interambulacral plates.
3. Apical disc compact, with five genital plates; periproct opening on the same surface as the peristome.
4. Fifth (posterior) genital plate pierced by a gonopore.
5. Internal radial buttresses developed along the adradial margins of interambulacral zones.