The eastern outskirts of Fennoscandia harbour two protected areas – Vodlozersky and Kenozersky national parks. They are relatively close to each other and occupy vast taiga territories in the Republic of Karelia and the Arkhangelsk Region. They are distinguished for the share of old-growth forests and the pattern of agricultural use of the land. The species composition of bats in these protected areas has not been previously studied, and the only species definitely known to inhabit the territories was the Northern bat. Special censuses of bats in these areas were carried out using traditional (mist nets, visual observations) and modern (static ultrasonic detector) methods. The counts were carried out at fixed points, along car and water transects. A total of 28 bats of 4 species were captured (Northern bat Eptesicus nilssonii Keyserling & Blasius 1839, Daubenton’s bat Myotis daubentonii Kuhl 1817, Brandt’s bat M. brandtii Eversmann 1845, whiskered bat M. mystacinus Kuhl 1817), and records were made of 185 bats of 7 species (apart from the ones listed above they were the brown long-eared bat Plecotus auritus L. 1758, common noctule Nyctalus noctula Schreber 1774, parti-coloured bat Vespertilio murinus L. 1758, pond bat M. dasycneme Boie 1825, Natterer’s bat M. nattereri Kuhl 1817), and bats classified as Brandt’s/whiskered bats. The relative abundance (%) and relative density (ind./km of transect) of some species are reported, as well as the dominance of the northern bat in all the communities, which is characteristic of the middle taiga subzone in general. The northernmost summer habitats of the whiskered bat in the European North of Russia were identified. A comparative analysis of the two protected areas in terms of species composition, relative abundance and relative density of bats did not reveal any sharp differences in these parameters.