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The subgenus Pteronotus (naked-backed bats) comprises three species, P. davyi, P. fulvus, and P. gymnonotus, which are distinguished from other members of the genus Pteronotus by wing membranes that are fused along the dorsal midline and by skulls with noticeably upturned rostrums. Pteronotus davyi currently includes two morphologically differentiated subspecies, P. d. davyi and P. d. incae, with strikingly disjunct geographic ranges. Whereas the nominotypical form is found in Central America, the Caribbean coastal region of northern South America, and the Lesser Antilles, the subspecies P. d. incae is restricted to a small area in northwestern Peru; to date, the phylogenetic relationships of these nominal taxa have not been explored. In the present contribution, we employed analyses of mitochondrial gene sequences, morphometrics, and qualitative-morphological comparisons to provide new information on P. d. incae and place the taxon in a phylogenetic context. Our results suggest that the geographically disjunct populations of P. davyi are genetically very similar even though they are morphologically and ecologically distinct. Recognizing that speciation is a process with intermediate stages that merit formal recognition, we support the retention of incae as a valid subspecies of Pteronotus davyi.