The California myotis, Myotis californicus, and western small-footed myotis, Myotis ciliolabrum, are 2 morphologically similar bats which have had a complex taxonomic history due to intraspecific geographic variation across their sympatric distribution in western North America. Despite several published differences, field identification remains problematic in the southwestern United States. Mitochondrial cytochrome-b and control region fragments were amplified from tissue samples (n = 20) from Texas, Oklahoma, New Mexico, Arizona, Utah, and California to examine species boundaries and phylogenetic relationships. DNA sequences (1,184 bp) were used in parsimony and maximum-likelihood analyses. To corroborate species identification, cranial measurements from all specimens included in the molecular analysis along with additional specimens were analyzed statistically using principal components analysis (PCA). Individuals were designated either as M. californicus or M. ciliolabrum. Molecular analysis placed M. leibii within clades containing both M. californicus and M. ciliolabrum. In addition, sequence divergence and phylogenetic results do not recover distinct lineages for each species (M. californicus and M. ciliolabrum) as recognized by morphology. Our results suggest that these species have recently diverged, or alternatively that they are 1 phenotypically variable species. Based on network estimation of cytochrome-b haplotypes, phylogeographic structure is minimally represented between haplotypes with an east-west separation in the southwestern United States.