Summary The species composition and distribution of heterotrophic flagellates in freshwater biotopes of Matveev and Dolgii islands were investigated. Thirtyseven species and forms were identified. Paraphysomonas vestita and Spumella sp. were the most common species. Most flagellates belonged to cercomonads, diplomonads, choanoflagellates and kinetoplastids. Species richness in different habitats varied from 2 to 10 species. The curve "cumulative species number vs. sampling effort" does not flatten out, so the species list obtained should be considered as incomplete. Local species richness of moss biotopes is significantly higher than predicted by this curve, whereas local diversity of lake biotopes shows a significantly lower level. Our observations confirm previous studies maintaining that the majority of the heterotrophic flagellates have a worldwide distribution. The lower complexity of polar heterotrophic flagellate communities may be explained by poor sampling effort.