Data on species composition of ciliates in the small rivers at Khabarovsk and in southern Sakhalin Island are presented. Modified method of sampling was applied with using of samplers and “glass fouling” on the shallows of the rivers. More than 230 samples were collected in the small rivers at Khabarovsk and about 200 samples in the southern Sakhalin. Species composition of the ciliates was determined immediately after the sampling and repeatedly on nutrient media. In total, 86 species of ciliates are identified, mostly belonged to the classes Oligohymenophorea and Spirotrichea. Six eurybionts were found: Coleps hirtus, Paramecium caudatum, Dexiostoma campylum, Colpidium colpoda, Uronema nigricans, and Vorticella convallaria сomplex . The classes Armophorea and Phyllopharyngea were more diverse by species in the area at Khabarovsk but the class Spirotrichea - in southern Sakhalin. In general, faunas of ciliates in two surveyed regions are similar. The highest inter-regional similarity of the species composition is registered between the rivers at Khabarovsk and the Susuya River in Sakhalin (25-33 %, by Jackaroo) that is probably associated with a heightened level of pollution in the Susuya. Most of the species adapt to habitat rapidly, so they are found in different environments: among benthos, plankton, periphyton. Some patterns of the ciliocommunities are discussed.