Chromosomal, genic, and morphologic variation was examined among populations of Dipodomys agilis from southern California and Baja California, including populations previously recognized as D. antiquarius, D. paralius, and D. peninsularis. Populations with a diploid chromosomal number of 62 and a fundamental number of 110 were found north of San Gorgonio Pass, and those possessing a diploid number of 60 and a fundamental number of 116 were found to the south. Genic data also indicated a similar separation of northern and southern populations. Analyses of morphologic data revealed that populations in the north were significantly larger than those in the south for several characters. Considering the three data sets, there is considerable differentiation of populations north of San Gorgonio Pass from those to the south. Apparently, the terrain at San Gorgonio Pass, and possibly human habitation, has prevented genetic exchange between these populations for a sufficient period for differences between them to accumulate.