Amoebae of the genus Korotnevella are covered with scales, the structure of which is believed to be species–specific andallows distinguishing species reliably at the morphological level. We studied members of this genus in order to assess thegenetic 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 structureof these amoebae, we identified all isolates based on the light-microscopic morphology and scale structure and investigatedboth inter-strain and intra-strain polymorphism of Cox I and 18S rRNA genes. Results show that both genes provide congruentpatterns of population structure. The Cox I gene appears to be more reliable DNA barcode while the 18S rRNA gene showsan interesting pattern of polymorphism, which may represent phylotypes of amoebae. Local population of amoebae in everystudied species consists of a number of genetic lineages (phylotypes), some shared between the populations while others areunique to a local habitat.