Caves offer bats refuges for hibernation, breeding and other social events. Their quality is important for species distribution. The role of cave microclimate as well as other environmental factors influencing the distribution of cave-dwelling species, is poorly known. We tested the significance of cave variables (length, temperature, elevation, occurrence of water) and geographical location for the presence of bats during hibernation and the breeding season in five regions in Romania. To detect species' environmental relationships, we used canonical correspondence analyses for winter bat aggregations and principal components analysis for maternity colonies. We analysed the factors influencing the distribution of bats by using two sets of explanatory variables reflecting cave characteristics and geographical locations. Winter aggregation was divided into three groups: (1) bat species that prefer high temperatures (Rhinolophus euryale, Myotis cappacinii) and hibernate at a low altitude; (2) species ranging from mid- to high elevation and low temperature (Myotis myotis/oxygnathus group); (3) species that hibernate in large, cold cave systems with a constant flow of the water (Pipistrellus pipistrellus, Nyctalus noctula, Barbastella barbastellus). Maternity colonies were divided into those that select either high (rhinolophids) or low temperatures (My. myotis/oxygnathus and Miniopterus schreibersii). The most important factors influencing the distribution of bats are the temperature in caves and their geographical location. This information was combined with IUCN's Red List data as well as with the number of individuals occurring in caves with the aim of identifying the key sites for conservation. The majority of these sites, which also constitute the refuges for vulnerable species, are located in west and south-western Romania. Seven caves provide shelter throughout the year for 122 000 individuals of 14 species.