The endemic Madagascar flying fox Pteropus rufus is threatened by habitat loss at roost sites and hunting for bushmeat. There is no conservation plan for this species, even though it is categorized on the IUCN Red List as Vulnerable and plays an important role as a seed disperser. In the Mangoro valley of central eastern Madagascar we monitored roost occupancy and abundance of P. rufus on 15 occasions at six sites over a 12-month period and conducted a detailed assessment of eight roosts during July 2004. There was considerable monthly variation in bat abundance and only two sites contained bats during every visit. Three sites were occupied only between September and March and may act as maternity or nursery roosts. Evidence of hunting was found at three roosts, and fire and forest clearance are ubiquitous threats. Two roosts were in Eucalyptus plantations and six were in small (2.2 - 28.7 ha) isolated fragments of degraded, mid elevation dense humid forest. All roosts were outside protected areas but were within 20 km of relatively intact forest. Faecal analysis revealed a diet of native forest tree species, cultivated fruits and Eucalyptus flowers. P. rufus in the Mangoro valley, and elsewhere in Madagascar, appears to survive in human-impacted environments by the inclusion of exotic plants in its diet and the ability to move between roosts. We provide conservation recommendations for P. rufus at both local and national levels.