The current definition of Procolophonomorpha, as defined by Modesto, Scott, & Reisz (2009), is that of as a stem-based group containing Procolophon and all taxa more closely related to it than to Milleretta.

Lee 1995, 1996, 1997 argues that turtles evolved from pareiasaurs, but this view is no longer considered likely.

Rieppel and deBraga 1996 and deBraga and Rieppel, 1997 argue that turtles evolved from sauropterygians, and there is both molecular and fossil (Pappochelys) evidence for the origin of turtles among diapsid reptiles.

The following cladogram is simplified after the phylogenetic analysis of MacDougall and Reisz (2014) and shows the placement of Procolophonomorpha within Parareptilia and its interrelationships.

[1] Mesosaurus Millerosauria Australothyris smithi Feeserpeton oklahomensis Colobomycter pholeter Delorhynchus cifellii Acleistorhinus pteroticus Lanthanosuchus watsoni Microleter mckinzieorum Belebey chengi Eudibamus cursoris Nycteroleteridae Pareiasauria Abyssomedon williamsi Nyctiphruretus acudens Owenettidae Procolophonidae