The New Zealand long-tailed bat (Chalinolobus tuberculatus) is an endangered species which is now absent from many habitats where they were previously observed. However, population genetics studies have been hampered by the lack of reliable genetic markers. We have developed 13 microsatellite markers, and at least eight of these are suitable for population studies. Nine of these markers also cross-react with the closely related Australian species C. gouldii. These markers may prove of general utility in the genus Chalinolobus.