We studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats.