[1] Traditionally, the Anapsida are considered the most primitive subclass of amniotes, the ancestral stock from which Synapsida and Diapsida evolved, making anapsids paraphyletic.

More recent morphological phylogenetic studies with this in mind placed turtles firmly within diapsids,[2][3][4][5][6] or, more commonly, within Archelosauria.

[9][10][11][12][13] One molecular study, published in 2012, suggests that turtles are lepidosauromorph diapsids, most closely related to the lepidosaurs (lizards, snakes, and tuataras).

[17][18] Gauthier, Kluge and Rowe (1988) attempted to redefine Anapsida so it would be monophyletic, defining it as the clade containing "extant turtles and all other extinct taxa that are more closely related to them than they are to other reptiles".

Indeed, Gauthier, Kluge and Rowe (1988) themselves included only turtles and Captorhinidae in their Anapsida, while excluding the majority of anapsids in the traditional sense of the word from it.

[19] Tsuji and Müller (2009) noted that the name Anapsida implies a morphology (lack of temporal openings) that is in fact absent in the skeletons of a number of taxa traditionally included in the group.