The vertebrate skull is a complex structure that has been shaped over evolutionary time by competing selective forces. Here, we take a comparative approach to study how male skull shape varies in the diverse lizard clade, Sceloporus. Specifically, we used CT scans, geometric morphometrics, and phylogenetic comparative methods to compare the skull shapes of species that differ in body size and the presence of ventral coloration, a key communication trait of Sceloporus lizards. We found that males of smaller-bodied species possess elongated and narrow skulls with shallower snouts than do males of larger-bodied species, which possess shorter and more robust skulls. Additionally, we found that males of species with colorful ventral patches have larger and more robust skulls than do males of species that have lost the ventral patches over evolutionary time. Males with white bellies have elongated and narrow skulls. Our phylogenetic analyses infer larger body size optima for males of species that possess ventral coloration than those of species that have lost the ventral patch. By taking advantage of imaging technology and placing it in a comparative framework, we gain new insight on the evolutionary processes that shape phenotypic traits leading to the patterns of diversity seen today.