[2] Although Rhabdocoela is a highly supported group in molecular studies, there is no clear morphological synapomorphy that unites them.

All rhabdocoels have a bulbous pharynx, but this is shared with other flatworm groups, such as Neodermata, Lecithoepitheliata and some species of Prolecithophora.

[3] Some possibly identified synapomorphies are found in the ultrastructure of the protonephridial system, but similar constructions exist in other groups.

Another possible apomorphy is found in the ultrastructure of the sperm, which has a dense heel on the basal bodies during spermiogenesis, but some groups have lost this feature.

The group Kalyptorhynchia, previously a subgroup of Thyphloplanoida, appears to be the sister-group of most other rhabdocoels, which form a clade named Dalytyphloplanida.