The populations of Thomomys bottae in the southern part of the Baja California peninsula have been assigned to several subspecies, mainly because they are isolated and show some morphological differences. In order to assess the status of T. bottae in Baja California, we conducted a survey in all the possible habitats in lowlands of the southern part of the peninsula by collecting specimens and obtaining tissues for genetic analyses. From the 6 subspecies of T. bottae present in Baja California Sur, 560 specimens were collected from 42 localities. A continuous geographical distribution among all the previously described isolate subspecies was confirmed and analysis of variance, analysis of molecular variance, and phylogentic analyses do not show morphologic or genetic differences among groups of the subspecies T. b. anitae, T. b. imitabilis, T. b. incomptus, T. b. litoris, and T. b. magdalenae from the lowlands south of the Vizcaino Desert. Thus, we conclude that these are junior synonyms of T. b. anitae. T. bottae russeolus in the Vizcaino Desert is sufficiently morphologically, morphometrically, and genetically different to be considered as a distinct subspecies.