Karyotypes differences between two subspecies of Pacific kangaroo rat Dipodomys agilis (2N=62 in the north and 2N=60 in the south), combined with minor allozyme and morphological differences, resulted in their re-classification into two the agile kangaroo rat (AKR, D. agilis) and the Dulzura kangaroo rat (DKR, D. simulans) in 1997. The distribution of AKR is from Kern and Santa Barbara counties down to upland areas the San Gabriel, San Bernardino, and Santa Monica mountains, while DKR occurs at lower elevations south from the foothills of those mountains to northern Baja California. It has been proposed that these two species are potentially sympatric in the foothill region of the San Gabriel mountains. We tested the validity of their species level classification, as determined by genomic divergence and the absence of introgression. To this end, we sampled AKR/DKR populations along a ~100 km transect crossing the San Gabriel mountains and performed whole genome sequencing/resequencing. Our results showed that, although AKR is found north and south of the mountains, there was no evidence of hybridization with DKR, supporting the specific status of the taxa. The divergence time between AKR and DKR was estimated as 0.5 to 1 Mya, and there is no proof of secondary contact since then. These populations encompassed a substantial elevational range, and we examined patterns of intraspecific genetic differences potentially linked to elevation.