Monitoring of animals over extended periods provides valuable information about their ecology and behaviour. Marking methods have been proposed and successfully used for numerous species, and yet a reliable, inexpensive method has not been found for bats. Available methods, including wing bands and collars, have also caused injury, and, in some cases, lead to death. We propose wing tattoos as an alternative method, as this has been extensively used to mark small mammals in both laboratory and field conditions. Initially we used tattoo equipment from the Animal Identification and Marking System (AIMS™, Canada), but adapted this and bought commercially available tattoo equipment, for human use, to set up our own tattoo system. We captured and tattooed 7,711 bats from 12 species across four years at three locations in South Africa between January 2013 and December 2019. Of these animals a total of 439 were recaptured with one individual captured 2,465 days after the initial tattoo, indicating the longevity of this method. In a captive population of Rousettus aegyptiacus, wing tattoos had no measurable negative effect on the animals, with no deaths and no infections, and remained legible over 927 days. Wing tattoos offer a non-lethal, cost-effective and long-lasting method to mark bats and monitor populations over long distances.