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Here, we have examined Hox expression in alligator, the closest living relative of birds, and an archosaur with a more conservative body plan. Two differences in Hox expression between chick, alligator, and other tetrapods correlate with aspects of alligator or bird\u2010specific skeletal morphology. First, absence of a thoracic subdomain of <jats:italic>Hoxc\u20108<\/jats:italic> expression in alligator correlates with morphological adaptations in crocodilian thoracic segments. Second, <jats:italic>Hoxa\u20105<\/jats:italic>, a gene required to pattern the cervical\u2013thoracic transition, shows unique patterns of expression in chick, alligator, and mouse, correlating with species\u2010specific morphological patterning of this region. Given that cervical vertebral morphologies evolved independently in the bird and mammalian lineages, the underlying developmental mechanisms, including refinement of Hox expression domains, may be distinct. <jats:italic>J. Exp. Zool. (Mol. Dev. 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