Clark and Carroll (1973) provided a composite skull, added to the post-cranium in the top image. Five good skulls are known (three shown above) and they show a surprising amount of variety, but they still nest together. Here Protorothyris is shown with its closest derived taxa, Echinerpeton, the protodiapsids Orovenator and Mesenosaurus, and the basal synapsids, Archaeothyris and Aerosaurus. Note the great resemblance between Archaeothyris and Orovenator. The canine tooth comes and goes in these basal forms.
Protorothyris was a member of a new clade, the Protosynapsida, defined as Paleothyris, Hylonomus, their most recent common ancestor and all of its descendants (that includes all mammals and birds). The Protosynapsida includes the traditional Synapsida (sans Caseasauria), plus a clade of taxa with a synapsid opening that are in the lineage of the basal diapsid, Petrolacosaurus. The Protodiapsida is defined as Archaeovenator, Heleosaurus, their last common ancestor and all of its descendants. The diapsids shown here did not include lizards and their kin,