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While genetic exchange between nonsister species was traditionally considered to be rare in mammals, analyses of molecular data in multiple systems suggest that it may be common. Interspecific gene flow, if present, is problematic for phylogenetic inference, particularly for analyses near the species level. Here, we explore how to detect and account for gene flow during phylogeny estimation using data from a clade of North American Myotis bats where previous results have led researchers to suspect that gene flow among lineages is present. Initial estimates of phylogenetic networks and species trees indicate that subspecies described within Myotis lucifugus are paraphyletic. In order to explore the extent to which gene flow is likely to interfere with phylogeny estimation, we use posterior predictive simulation and a novel Approximate Bayesian Computation approach based on gene tree distances. The former indicates that the species tree model is a poor fit to the data, and the latter provides evidence that a species tree with gene flow is a better fit. Taken together, we present evidence that the currently recognized M. lucifugus subspecies are paraphyletic, exchange alleles with other Myotis species in regions of secondary contact, and should be considered independent evolutionary lineages despite their morphological similarity.