Bats are an endangered group of mammals and populations of several species have been declining for decades in Europa. Consequently all species are listed on the European Habitats Directive. One of the obligations of this Directive is that member states must report on the conservation status of the species and habitats (article 17). In this article we discuss the conservation status of the bat species in the Flemish region. The assessment of the conservation status is based on the range, the size and the trend of the population, the habitat and the future prospects for each species. Although bats are elusive animals and data is sparse, we can conclude that only five species have a favourable conservation status. Since the implementation of the Habitats Directive one species, the Barbastelle bat has gone extinct, while the ranges of Geoffroy’s bat, Pond bat and Greater mouse-eared bat have markedly decreased. Also more common species, such as Daubenton’s bat and Noctule, are decreasing. The big seasonal difference in the trends and numbers of population of Geoffroy’s bat and Pond bat are striking. Numbers of both species are increasing in protected hibernation sites, but summer populations are decreasing and are under great pressure. This shows that caution is needed when interpreting the data form hibernation census counts. For an adequate monitoring, more data on the summer populations is needed. Conservation measurements need to take all elements used by bats in their complex life-cycles into account: summer roosts, hibernation and swarming sites, foraging areas and the connections between these.