Abstract: Recognizing delineations of gene flow among groups of animals can be challenging, but necessary for conservation and management. Of particular importance is the identification of species boundaries. Several physical and genetic traits have been used with mixed success to distinguish Myotis keenii (Merriam, 1895) (Keen’s myotis) and Myotis evotis (H. Allen, 1864) (long-eared myotis), but it is unclear whether species distinction is biologically warranted. We generated 12-14 microsatellite loci genotypes for 275 long-eared Myotis representing 4 species -- M. keenii, M. evotis, Myotis septentrionalis (Trouessart, 1897) (northern myotis), and Myotis thysanodes Miller, 1897 (fringed myotis) -- from across northwestern North America, and 23 Myotis lucifugus (Le Conte, 1831) (little brown myotis) as outgroup. Population genetics analyses revealed four well defined groups (species): M. septentrionalis, M. thysanodes, M. lucifugus and a single group comprising M. keenii and M. evotis. We document high rates of gene flow within M. evotis/keenii. Cytochrome b gene (mtDNA) sequencing failed to resolve morphologically identifiable species. We highlight the importance of geographically thorough investigation of genetic connectivity (nuclear markers) when assessing taxonomic status of closely related groups. We document a morphometric cline within M. evotis/keenii that may in part explain earlier analyses that led to the description of the smaller-bodied M. keenii (type locality Haida Gwaii). We conclude that M. keenii does not qualify as a genetic or biological species.