Desert shrews of the genus Notiosorex comprise four species with morphological characteristics that are difficult to distinguish among the species. Indeed, N. cockrumi was described using only genetic markers. Based on molecular divergence documented in N. crawfordi, we hypothesize that a fifth species is present in the Baja California peninsula. Genetic variation at the species level was analyzed using individuals from locations west of the Colorado River in the Baja California peninsula, Mexico, and California, United States. Molecular markers of mitochondrial origin (cytochrome b, 1,140 bp; cytochrome c oxidase subunit I, 542 bp; and cytochrome c oxidase subunit III, 672 bp), as well as the nuclear intron 7 of the beta fibrinogen gene (385 bp) were used to construct a phylogeny for species of the genus Notiosorex. Genetic distances of 12.46–15.58% between west and east of the Colorado River were obtained using p-distance models. Our phylogenetic analyses showed almost identical topologies, placing populations from west of the Colorado River in three monophyletic clades with high bootstrap support values. Results of molecular phylogenetic identity among shrews of the genus Notiosorex support the existence of an undescribed, polytypic species of Notiosorex west of the Colorado River.