Myotis peninsularis Miller, 1898 is an endemic bat from the Cape Region in Baja California Sur, México. Its taxonomic status is unclear, either as a valid species or as a subspecies of M. velifer (J. A. Allen, 1890). In order to assess its taxonomic status, the objective of this study was to examine phylogenetic relationships of M. peninsularis, using molecular and geometric morphometric data. Two mitochondrial genes were analyzed: cytochrome oxidase subunit I (COI) and cytochrome b (Cytb). The phylogenetic analysis (maximum likelihood and Bayesian Inference) showed that M. peninsularis and M. velifer were sister groups, collectively forming a monophyletic assemblage. We observed less than 2% of genetic distance in the Cytb, considered an interval at the subspecies level. The geometric morphometric analysis showed differences in skull shape. We obtained three morphotypes: M. peninsularis (Baja California group), M. velifer incautus (northern population) and M. v. velifer (southern population). The most important differences were located in the braincase (ventral, dorsal and lateral view). The lateral view was the most discriminating. The Cape Region specimens had the sagittal crest more procumbent in the front than the rear of the braincase. The slope line at the rostral lateral view was more abrupt in M. velifer populations. Morphologically, the three lineages tended to possess the same normal variation as the entire Mexican population of M. velifer but with a specific morphotype associated to its distribution. In a combined molecular and landmark configuration of the phylogenetic analysis, the ancestral shape corresponded to an intermediate shape between M. peninsularis and M. velifer, presenting a similar variation to the one of intra-specific level in M. velifer. We considered M. peninsularis a junior-synonym of M. velifer.