The validity of Myotis occultus as a species unique from M. lucifugus has been a source of debate. Most recently, many authorities treat M. occultus as a distinct species, at least in part because a previous study showed that M. occultus and M. l. carissima (the subspecies that occurs in closest proximity to M. occultus) form separate monophyletic clades based on sequences of two mitochondrial genes (cytochrome-b [cytb] and cytochrome oxidase subunit II [COII]). We re-evaluated the phylogenetic relationship between M. occultus and M. lucifugus based on mitochondrial sequences using an expanded dataset of cytb and COII sequences that originated from more genetically diverse specimens of M. lucifugus collected across a broader geographic area. Based on a phylogenetic analysis, we found that M. occultus sublineages were embedded within a well-supported clade that included some specimens of M. lucifugus. These results indicate that the previous genetic analysis demonstrating that M. occultus and M. lucifugus form distinct monophyletic groups is unsupported by our larger dataset. Future genetic work involving whole genome sequencing of nuclear DNA will likely be needed to better resolve the true taxonomic relationship between M. occultus and M. lucifugus.