We investigated the distribution and abundance of the bats from the undergrounds in Moldavia and Dobrogea. Data was collected during 2002-2010. There were identified 20 species of bats (3-12 species/cave). In the undergrounds from Moldova area the dominating species are Myotis myotis/Myotis oxygnathus (71,5%), and in Dobrogea, Myotis oxygnathus (41,1%), Myotis daubentonii (24,1%), and Miniopterus schreibersii (16,7%). The most important underground shelter is the Bats Cave from Rarău Mountains, which hosts a wintering colony of 3500-3700 individuals of Myotis myotis/Myotis oxygnathus, and in the warm season shelters 10 species of bats. We analyzed the microclimate preferences (for temperature and humidity), during hibernation, at 15 species of bats. Nowadays, from the undergrounds studied, only the Bats Cave from Rarău has an adequate protection and some populations of bats are seriously threatened or have disappeared.