Amoebae of the genus Korotnevella are covered with scales, which are believed to be species–specific and allow reliable distinguishing of species at the morphological level. We studied members of this genus in order to access the genetic structure of the local populations of amoebae. For the present study we isolated nine freshwater strains of Korotnevella, belonging to three species, from two locations in North-Western Russia. In order to obtain data on the population structure of these amoebae we identified all isolates basing on the morphology and investigated both inter-strain and intra-strain polymorphism of Cox I and 18S rDNA genes. Results show that both genes provide congruent pattern of the population structure; Cox I gene appears to be more reliable DNA barcode while 18S rDNA gene shows interesting pattern of polymorphism, which may represent phylotypes of amoebae. Local population of amoebae in every studied species consists of a number of genetic lineages (phylotypes), some shared between the pop