We visited four cave roosts of the near threatened, and endemic, fruit bat Rousettus madagascariensis over a five year period and found major threats to the bats from hunting and deforestation. The conservation of this species is particularly challenging because it is legally hunted inside its cave roosts. Although provisional protected area status was obtained for two sites with community support, hunting continued. R. madagascariensis roosts were associated with humid forest and the loss of vegetation around caves rendered them unsuitable for the bats at two abandoned sites. A few individual hunters can have a rapid and destructive impact on R. madagascariensis roosts and future initiatives in this area should involve working with hunters to develop realistic solutions to reduce hunting. These efforts need to be supported by habitat protection measures.