In this thesis we studied distribution of species from a morfologicaly criptic complex Niphargus stygius. We studied 94 individuals from 38 localities and successfully isolated DNA and amplified subunit I of mitochondrial gene for cytochrome oxidase (COI) in 62 individuals. The sequencing unveiled six, one, eight, two, one and two new localities for N. chagankae, N. cvajcki, N. gottscheeanensis, N. kenki, N. malagorae and N. zagrebensis, respectively. The new records substantially expanded the known distributions of N. gottscheeanensis and N. kenki. We recorded the first case of the coexistence of N. chagankae and N. likanus, and another case of coexisting N. gottscheeanensis and N. podpecanus. Additionally, we estimated potential species' distributions using climate data in the programme MaxEnt. We ran two models of different complexity, based on mean annual temperature and overall annual precipitation, and, alternatively, based on mean annual temperature, annual minimal and maximal monthly temperature, maximal, minimal and overall annual precipitation. The models successfully applied only in species with eight or more records (N. chagankae, N. gottscheeanensis, N. stygius) and more complex model outperformed the simpler one. However, the models do not correspond to to real distributional data, suggesting that our models likely missed key determinats of species' distribution.