Anapsid systematics, like that of most other groups of organisms, is still in a state of flux because the phylogeny of this group is still controversial. The origin of turtles has been debated: procolophonids and pareiasaurs have both been argued to be their closest known relatives. Pareiasaurs have even been argued to be the stem-group of turtles, but this implies that some pareiasaurs survived the End Permian extinction event (about 250 million years ago) and evolved into turtles by the Upper Triassic (about 210 million years ago). However, pareiasaurs, procolophonids, and turtles certainly form a clade that excludes other known anapsids.
The relationships of more basal anapsids are not firmly established, but millerettids apparently appeared first. Recent work suggests that the Lower Permian anapsid Acleistorhinus is closely related to lanthanosuchids, and that these two taxa are more closely related to turtles than to millerettids.