The species composition and morphology of heterotrophic flagellates collected from mire hollows, flowing waterlogged mire sites, mire pools, streams, and watercourses were studied in Pinega district, Arkhangelsk region, Russia. Fifty species of flagellates belonging to four macrotaxonomic clusters were recorded. Most of the flagellates were bacterivorous; two species were predators, and two species were omnivorous. Each type of mires and mire waterbodies has a particular set of species (ANOVA: F = 15.5, p< 0.001). Thirty-four species of heterotrophic flagellates were found in eutrophic mires (interhummock spaces and streams), and 26 species inhabited oligotrophic mires (mire hollows, streams, and pools). The protist fauna was extremely poor in mire pools (two species). Nonparametric MDS-analysis revealed four groups of communities: (1) mire hollows and waterlogged mire sites; (2) interhummock spaces, mire hollows, and streams; (3) degrading hollows-rimpi; (4) mire pools. The species richness depended on electric conductivity of the water (τ = 0.65, p = 0.002). Descriptions, drawings and pictures showing the details of cell structures are given for the most poorly studied species. All the species recorded are new for the fauna of Arkhangelsk region.