Information on the bat fauna of the Andaman and Nicobar Islands was limited previously to the results of sporadic surveys, with no specific focus on the habitats or distribution of the species. We carried out the first extensive survey of the Andaman and Nicobar Islands during 2003–2006, covering 40 islands. Our objective was to map the bat species, their habitats and distribution. This resulted in identification of 25 bat species representing 13 genera, location of > 300 roosts and validation of previously recorded species. Notable findings included the rediscovery of the endemic Nicobar flying fox Pteropus faunulus after a century and its extinction from the type locality on Car Nicobar Island, the sighting of an albino Hipposideros diadema nicobarensis from Katchal Island, and the first records of Rhinolophus yunanensis, Murina cyclotis and Hipposideros larvatus from the Andaman Islands, and Taphozous melanopogon, Murina cyclotis, Pipistrellus spp., Myotis horsfieldii dryas and Cynopterus brachyotis from the Nicobar Islands. Threats to the bat fauna appear to be primarily roost disturbance and hunting for sport. Anthropogenic pressure on species of Pteropus is high as hunting occurs throughout the year. Secondary sources and our field observations confirmed the decline of Pteropus in several islands as a result of hunting and alteration to habitats. We introduced a community initiative to monitor and protect roosts and foraging sites close to settlements in the Nicobar Islands. Priorities identified for conservation of the bat fauna of the archipelagos are mitigation of threats to flying foxes and cave dwelling bats, initiation of research on endemic bat species such as P. faunulus, and a voluntary ban by local communities on hunting in specific areas and seasons.