Several data partitions, including nuclear and mitochondrial gene sequences, chromosomes, isozymes, and morphological characters, were used to propose a new phylogeny and to test previously published hypotheses about the phylogenetic positions of basal clades of the lizard genus Sceloporus and the relationship of Sceloporus to the former genus "Sator". In accord with earlier studies, our results grouped "Sator" internal to Sceloporus, and both support a hypothesis of transgulfian vicariance for the origin of the former genus "Sator" on islands in the Sea of Cortez. Robustness of support for internal nodes in our best tree was established though widely used indices (bootstrap proportions, decay values) but also through congruence among independent data partitions. Several deep nodes in the tree recovered by a number of methods, including equally weighted and differentially weighted parsimony, and maximum likelihood models, are only weakly supported by the traditional indices, and this methodological concordance is taken as evidence for insensitivity of the deep structure of the topology to alternate assumptions.