The Livingstone's fruit bat Pteropus livingstonii is endemic to the small islands of Anjouan and Mohéli in the Comoros archipelago, Indian Ocean. The species is under threat from anthropogenic pressure on the little that remains of its forest habitat, now restricted to the islands’ upper elevations and steepest slopes. We report the results of the most comprehensive survey of this species to date, and present recommendations for ongoing field conservation efforts and monitoring. Morning counts were conducted at roost sites in the wet and dry seasons during 2011–2013. Habitat structure around the roosting sites was characterized and roost numbers compared, to investigate the potential effect of habitat loss and degradation. We estimate the population to comprise c. 1,260 individuals distributed across 21 roosts on the two islands. All occupied roosting sites were restricted to a narrow altitudinal range, and roosting populations in agroforestry areas were smaller than those found in degraded and undisturbed forest. Only one of the 16 roosts on Anjouan was found in undisturbed, old-growth forest with no nearby signs of clearance for agriculture or landslides following tree-felling upslope. Following a suspected severe population decline as a result of widespread and long-term forest loss Livingstone's fruit bat has been recategorized as Critically Endangered on the IUCN Red List.