Proterochampsians share several distinguishing characteristics, or synapomorphies. A prominent ridge runs along the length of the jugal, a bone below the eye. Another ridge is present on the quadratojugal, a bone positioned toward the back of the skull behind the jugal. There is also a depression on the squamosal bone of the skull roof. The second metatarsal of the foot is wider than the other metatarsals. Proterochampsians lack a fifth digit on the foot; the fifth metatarsal is reduced to a small pointed bone.
Below is a cladogram showing the phylogenetic relationships of proterochampsians from Kischlat and Schultz (1999):
Dilkes and Arcucci (2012) combined data from several phylogenetic analyses of the Archosauriformes, such as Dilkes and Sues (2009), Ezcurra et al. (2010) and Nesbitt (2011), and added ten new characters to their matrix. The monophyly of Proterochampsia was supported by 12 unambiguous synapomorphies in their analysis, including the presence of dermal sculpturing on skull that consists of prominent ridges or tubercles on frontals, parietals and nasals; a contact between the maxilla and the prefrontal, separating lacrimal and nasal; a strongly convex dorsal margin of surangular and palatal teeth that are inserted into alveoli. Some of the synapomorphies recovered by Nesbitt (2011) were found to support either the node Cerritosaurus + Chanaresuchus or the node Tropidosuchus + Chanaresuchus. One possible proterochampsian genus, Rhadinosuchus, was excluded from their analysis pending a re-examination of its holotype. According to Dilkes and Arcucci (2012), although Rhadinosuchus might not be valid, it shares some traits with derived proterochampsians like Chanaresuchus. The cladogram below follows their analysis.
Trotteyn and Haro (2012) conducted a phylogenetic analysis of proterochampsians and other basal archosauriforms using only braincase characters, and found Doswellia, an unusual long-necked, heavily armored archosauriform from Virginia, to nest within Proterochampsia. A close relationship between Doswellia and proterochampsids was also found by Benton and Clark (1988) and Dilkes and Sues (2009). Trotteyn and Haro (2012) considered Proterochampsia to include proterochampsids and Doswellia, and proterochampsids to include all proterochampsians more closely related to Proterochampsa than to Doswellia.
^Dilkes, D.; Arcucci, A. (2012). "Proterochampsa barrionuevoi (Archosauriformes: Proterochampsia) from the Late Triassic (Carnian) of Argentina and a phylogenetic analysis of Proterochampsia". Palaeontology55 (4): 853–885. doi:10.1111/j.1475-4983.2012.01170.x.edit
^Trotteyn, M. A. J.; Haro, J. A. (2012). "The braincase ofChanaresuchus ischigualastensis(Archosauriformes) from the Late Triassic of Argentina". Journal of Vertebrate Paleontology32 (4): 867. doi:10.1080/02724634.2012.670178.edit