SummarySpecies diversity and morphology of heterotrophic flagellates from 5 primary mire lakes and 4 secondary hollow-pools in mires were studied. Samples were taken from three microbiotopes: plankton, benthos, and periphyton. Micrographs and morphological descriptions for all observed species were given. A total of 40 species and forms were found. The most common species were Bodo saltans, Goniomonas truncata, Neobodo designis, Rhynchomonas nasuta, and Ancyromonas sigmoides. The higher species richness, as well as the greater number of unique species was registered in primary mire lakes. Bodo saltans, Neobodo designis, and Spumella sp. were found in all types of the studied microbiotopes. Greater species diversity was discovered in benthos.