Aetosaur phylogeny was first investigated in 1994 by paleontologist J. Michael Parrish. Aetosauroides, Aetosaurus, Desmatosuchus, Longosuchus, Neoaetosauroides, Stagonolepis, and Typothorax were included in the phylogenetic analysis. Aetosaurs were found to form a clade with rauisuchians, which Parrish termed Rauisuchiformes. Rauisuchiformes also included the superorder Crocodylomorpha, to which living crocodilians belong. Parrish found Aetosauria to be a monophyletic group and thus a true clade consisting of a common aetosaur ancestor and all of its descendants. To phylogenetically define Aetosauria, Parrish identified five synapomorphies, or shared characteristics. The first synapomorphy concerned the jaw, with the premaxilla at its tip being edentulous, upturned, and wide to form a "shovel". Moreover, the dentary bone in the lower jaw is also toothless, upturned, and broad. The reduced size and simple conical shape of the teeth was considered another synapomorphy. Two more synapomorphies of aetosaurs are shared with crocodylomorphs, but were not considered to be an indication of a close phylogenetic relationship; the body is covered in dorsal and ventral armor to form a complete carapace, and the paramedian osteoderms are much wider than they are long, with distinctive pitting. A final synapomorphy was found in the structure of the limb bones. In all aetosaurs, the limbs are very robust, with large muscle attachments such as the deltopectoral crest of the humerus, the fourth trochanter of the femur, the intracondylar ridge of the tibia, and the iliofibularis trochanter of the fibula.
In Parrish's phylogenetic analysis, Aetosaurus was found to be the most basal member of the clade, the earliest to diverge after the most recent common ancestor. After Aetosaurus, there is a polytomy of three smaller clades in which it is unknown which clade diverged first from the group. Within this polytomy there was Neoaetosauroides, a clade containing Aetosauroides and Stagonolepis, and another polytomy that included Longosuchus, Desmatosuchus, and a clade containing Paratypothorax and Typothorax.
A later study by paleontologists Andrew B. Heckert and Spencer G. Lucas in 1999 expanded the number of synapomorphies that diagnose Aetosauria to 18. New synapomorphies included temporal fenestrae, or holes, that opened on the side of the skull rather than the top, lateral osteoderms articulating with the paramedians, and osteoderms covering the limbs. Aetosaurus was still found to be the most basal member, but the phylogeny of more derived aetosaurs differed in that Typothorax and Paratypothorax were split into two different clades with their sister taxa being Desmatosuchus and Longosuchus, respectively. More importantly, a new aetosaur called Coahomasuchus was included in the analysis. Coahomasuchus was found to be a basal aetosaur closely related to Stagonolepis, and also appeared early in the fossil record of aetosaurs. Previously, basal members were only known from later times, occurring after more advanced aetosaurs.
In 2003, paleontologists Simon R. Harris, David J. Gower, and Mark Wilkinson examined previous phylogenetic studies of aetosaurs and criticized the way in which they used certain characters to produce cladograms. They concluded that only three hypotheses of aetosaur relationships from previous studies were still true: that Aetosaurus is the most basal aetosaur, that Aetosauroides is the sister taxon of Stagonolepis robertsoni, and that Longosuchus and Desmatosuchus are more closely related to each other than either is to Neoaetosauroides. They also went on to correct the trees from all previous analyses.
More recently, a 2007 analysis by paleontologist William G. Parker resulted in a larger tree of aetosaur phylogenetics with the inclusion of Heliocanthus. Based on the tree, Parker defined the clades Typothoracisinae and Paratypothoracisini, both within Aetosaurinae. Parker also gave a revised phylogenetic definition of Aetosauria, mentioning that the previous definition, made by Heckert and Lucas in 2000, was somewhat ambiguous. Heckert & Lucas (2000) defined Aetosauria as a stem-based taxon, claiming that Aetosauria included all crurotarsans that were more closely related to Desmatosuchus than to the immediate sister group of Aetosauria. Because the immediate sister group of Aetosauria was uncertain, Parker offered a new definition with several non-aetosaur crurotarsan genera rather than one sister group. According to Parker, Aetosauria included all taxa more closely related to Aetosaurus and Desmatosuchus than to Leptosuchus, Postosuchus, Prestosuchus, Poposaurus, Sphenosuchus, Alligator, Gracilisuchus, and Revueltosaurus.
In 2008, Parker, along with Michelle R. Stocker and Randall B. Irmis, conducted a new phylogenetic analysis which included the newly described Sierritasuchus. Below is the cladogram from Parker et al. (2008):
A new genus of aetosaur, Aetobarbakinoides, was named in 2012. The phylogenetic analysis in that study found Aetosaurinae to be a paraphyletic grouping. As a paraphyletic group, aetosaurines would share a most recent common ancestor that is also the ancestor of other non-aetosaurine aetosaurs, and thus could not form their own clade. Parker's 2007 analysis accepted this definition. In 2002, Heckert and Lucas defined Aetosaurinae as "a stem-based taxon containing all taxa more closely related to Aetosaurus than to the last common ancestor of Aetosaurus and Desmatosuchus". The 2012 study placed Aetosaurus at the base of the stagonolepidid clade, with traditional aetosaurine taxa placed in successively more derived positions. In the analysis, these taxa are actually more closely related to Desmatosuchus than to Aetosaurus. Thus, under Heckert and Lucas's definition Aetosaurinae might be restricted to only Aetosaurus itself.
Another finding of this study was that Aetosauroides lies outside Stagonolepididae. If this phylogeny is correct, Stagonolepididae and Aetosauria would not be equivalent groupings, and Aetosauroides would be the first non-stagonolepidid aetosaur. The following cladogram simplified after an analysis presented by Julia B. Desojo, Martin D. Ezcurra and Edio E. Kischlat (2012).
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