Polydactyly in bats has rarely been observed; a few cases are recorded for insectivorous molossid and vespertilionid species in North America. Here we report polydactyly in the foliage-roosting phyllostomid Artibeus lituratus, in the southern Pantanal floodplain and adjacent uplands, Brazil. Bats were mist-netted in six populations, and capture rate per population was estimated. Of 444 A. lituratus individuals sampled, one female and one male exhibited supernumerary toes. These cases occurred in the two densest populations, in sites where forests are distributed in small disconnected fragments. This situation could favour increased inbreeding in A. lituratus and, indirectly, the manifestation of polydactyly.