Phylogenetic relationships of the whiptail lizards of the genus Cnemidophorus are inferred based on a combined analysis of mitochondrial DNA, morphology, and allozymes. Within the Teiini, Teius and Dicrodon are the most basal lineages, and these two taxa form a graded series leading to a cnemidophorine clade containing Ameiva, Cnemidophorus, and Kentropyx. Cnemidophorus monophyly is not supported, with members of the neotropical “C” lemniscatus species group (except “C” longicaudus) being more closely related to species in other neotropical cnemidophorine taxa (Ameiva and Kentropyx). Ameiva is also paraphyletic.

The “Cnemidophorus” lemniscatus species group is also paraphyletic, with a “C” murinus “C” lemniscatus complex clade being more closely related to Kentropyx than to “C” lacertoides, “C” longicaudus, and/or “C” ocellifer. Although the “C” lemniscatus species group is paraphyletic, the three remaining bisexual “Cnemidophorus” species groups (deppii, sexlineatus, and tigris species groups) are each monophyletic. Together, these three groups form a clade (= North American “Cnemidophorus” clade), with the deppii and tigris species groups being sister taxa. Within the “Cnemidophorus” deppii species group, the Baja California “C” hyperythrus is the sister species to a more exclusive mainland Mexico clade containing “C” deppii and “C” guttatus. Except for a “C” inornatus “C” sexlineatus clade and a monophyletic “C” gularis complex, the inferred inter- and intraspecific relationships within the sexlineatus species group are weakly supported. In none of the inferred phylogenies are the “C” costatus populations (“C” c. costatus and “C” c. griseocephalus) represented as each other's closest relatives.

Because of Cnemidophorus paraphyly, nomenclatural changes are recommended. Aspidoscelis Fitzinger, 1843, is resurrected for the North Americ