Multivariate analyses of seven meristic characters from 257 specimens of Aspidoscelis hyperythra from Baja California Peninsula, Mexico, revealed pan-peninsular patterns of morphological variation. We observed a significant morphological shift between southern and northern populations at the Isthmus of La Paz, the location of a Pliocene trans-peninsular seaway that could have separated the two groups for a substantial length of time. However, we did not observe fixed character states, such as number of pale dorsal stripes, diagnostic of southern and northern populations. The co-occurrence in local populations of variable numbers of individuals with five, six, or seven stripes makes peninsular A. hyperythra an unusual member of the A. deppii species-group, where number of stripes is consistent in local populations. Samples from the Cape Region were statistically homogeneous based on the characters analyzed, but samples from the latitudinally expansive northern area revealed a pattern of similarities and significant differences unrelated to distances between localities.