Species diversity of centrohelid heliozoans in different types of freshwater bodies (forest lakes, floodplain lakes, sphagnum bogs, and river) in the Middle Russian forest-steppe was studied. The morphology of cell coverings (scales and spicules) were observed using scanning and transmission electron microscopy. A total of 20 species of centrohelid heliozoans from five families (Acanthocystidae, Pterocystidae, Raphidiophryidae, Raphidocystidae, and Choanocystidae) and six genera (Acanthocystis, Raineriophrys, Pterocystis, Raphidiophrys, Raphidocystis, and Choanocystis) as well as unidentified Centrohelea species and a Heterophrys-like organism were found. Morphological descriptions and electron micrographs are provided. The most common species were Acanthocystis nichollsi, Raphidiophrys capitata, and a Heterophrys-like organism. The highest species diversity was observed in terrace forest lakes, whereas the lowest was seen in sphagnum bogs. Four species (Acanthocystis costata, A. elenazhivotovae, A. mikrjukovii, and A. spinosa) were found for the first time since their original description. Three species (Acanthocystis spinosa, Raphidiophrys capitata, and Pterocystis pulchra) are new records for Russia. The distribution of the observed morphospecies confirms the cosmopolitanism of many centrohelids and highlights the importance of the type of water body and microbiotope in forming the species composition. The obtained data on the morphology of studied scales supplements our knowledge of the intraspecific variability of centrohelid heliozoans.