Sardinia is home to three bat species of chief conservation importance, the endemic Plecotus sardus as well as Myotis punicus and Rhinolophus mehelyi, for which Sardinia is the Italian stronghold. We carried out two gap analyses overlapping the network of protected areas present on the island respectively with 1) the occurrence records of all species and 2) the binarized maps obtained from maximum entropy models. Unlike the other two species, P. sardus known records are confined to the central sector of the island and its suitable habitat partly overlaps with that of M. punicus but not with R. mehelyi. Due to its uniqueness and restricted range P. sardus requires a very specific management strategy for its protection to be successful. Both analyses led to the conclusion that all species considered require more extensive protection than is currently granted so that urgent measures should be taken to improve the current situation.