Puerto Rico, the easternmost island in the Greater Antilles, is home to 13 species of bats, representing five families—Molossidae, Mormoopidae, Noctilionidae, Phyllostomidae, and Vespertilionidae. The purpose of this study was to determine whether species found on Puerto Rico could be differentiated based on external hair morphology, using the scanning electron microscope. Hair samples were taken from the dorsal mid-scapular region of one-to-four bats of each species. For consistency and repeatability, we examined the area between 550 and 800µm from the hair tip for all samples; however, an additional segment between 120 and 200µm from the tip was needed to differentiate two species in Phyllostomidae. Each species demonstrated distinct qualitative traits that allowed identification based on hair alone. Practical uses of this technique would be to identify hair samples taken from archaeological sites or to determine which species of bat once occupied now-abandoned roosts. In addition, analysis of hair found in owl pellets or the feces of mammalian carnivores, could be used to examine predator-prey interactions, even if no skeletal remains were present. We suggest that examination of hair under the scanning electron microscope could help differentiate among species in other simple assemblages of bats, such as those on different islands or restricted areas of continents, and perhaps use of this technique as a broader taxonomic tool should be revisited.