Pigmentation anomalies and lesions are aspects of wild bat populations that have been rarely addressed and scarcely documented. We captured a total of 4,118 bats belonging to 30 species during 2020, 2021, and 2022 in the municipalities of Santa Maria Huatulco and San Miguel Lachiguiri, Oaxaca, southeastern Mexico. Of these, 9 individuals (0.21 %) showed piebaldism (6 females and 3 males), and 11 individuals (0.26 %) had skin and hair lesions (7 females and 4 males). The highest number of piebaldism and lesions was observed in Natalus mexicanus (6 of the 20 individuals), followed by Mormoops megalophylla (n = 4), Pteronotus mesoamericanus (n = 3), Pteronotus fulvus (n = 3), Glossophaga mutica (n = 2), and Artibeus lituratus (n = 2). The months with the highest number of bats with piebaldism and lesions were October (n = 6) and July 2021. Seventeen records occurred in caves, two in the medium sub-evergreen forest, and one in a human settlement. To date, it has not been confirmed that skin depigmentation in bats affects the social life and reproductive activity of bats, but they could be more susceptible to predation events. Furthermore, lesions could negatively affect flight performance and, consequently, foraging efficiency.