In the Czech Republic, P. pipistrellus sensu lato was considered a common bat species in the past, distributed over the majority of the state area. Recently two species of common pipistrelles, P. pipistrellus sensu stricto and P. pygmaeus are distinguished and both cryptic species occur in the Czech Republic, but their geographical and altitudinal distribution pattern has hitherto not been recognized. We summarized all former data about occurrence of all common pipistrelles at first, especially sites of nursery colonies. All sites we included to the grid map of the Czech Republic divided into 695 quadrats of 6 x 10 (approximately 11.2 x 12 km, 134 km2) unified to all faunistic researches in the Czech Republic. A database of former undistinguished records (up to 2001) consists of 1531 records of P. pipistrellus sensu lato in 155 quadrats (22.3% of the Czech Republic). Since 2002 the research project has been started to map the distribution of both pipistrelles separately using mainly bat-detectors. Bat-detectoring in line transects has been performed in suitable habitats, especially at watersides, edges of growth and illuminated intravilans in human settlements of each mapping square visited. In each mapping quadrat two or more sites were selected so that the total duration of recordings was 60 minutes at least. Most records have been confirmed later by PC analyses of time expension or frequency division recordings of bat echolocation (search phase) or social calls using BatSound software, and some of them also by genetic analyses of tissue samples. Hitherto, 184 sites of P. pipistrellus sensu stricto in 151 mapping quadrats (21.7%) and 100 sites of P. pygmaeus in 60 quadrats (8.6%) have been found. While P. pipistrellus s. s. has been recorded almost in the whole territory except at high elevations, the range of P. pygmaeus is considerably lesser and the main area of its distribution is that in lowlands of Moravia and C-Bohemia and in basins of S-Bohemia. P. pygmaeus especially prefers floodplain forests and other wetlands in the aluvium and a pond landscape in the basins where it prevails sympatric P. pipistrellus s. s. The area of the Moravian population of P. pygmaeus continues towards the south in SW-Slovakia and N-Austria and in the north it is spread to lowlands of S-Poland probably. Most records of P. pygmaeus come from low altitudes (150-200 m a. s. l., max. 450 m a. s. l.) whereas P. pipistrellus s. s. has been recorded up to 862 m a. s. l. and it does not avoid wooded highlands or human settlements contrary to former species. Allopatric populations of P. pipistrellus s. s. seem to be that in mountains and highlands of the nothern part of state territory and in W-Bohemia and E-Moravia. The research was supported by the grant of the Czech Science Foundation No. 206/02/0961, the grant of Ministry of Education, Youth and Sports of the Czech Republic No. MSM 0021622416 and the Czech Bat Conservation Trust.