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The taxonomic composition of the bacteriobenthos of the littoral and pelagic zones of the Lake Kandry-Kul’ was analyzed by gas chromatography-mass spectrometry (microbial markers). The studied communities comprise 39 taxa of the Bacteria domain. Two dominant taxa were a characteristic of bacteriobenthos in the littoral zone in June, one dominant taxon, in September. The taxonomic structure of bacteriobenthos of the pelagic zone was characterized by two dominant taxa both in June and September. There were common dominants in the littoral and pelagic biotopes, namely, representatives of the genera Butyrivibrio, Spirochaeta, and of the group of iron-reducing bacteria (FeRB). The species Clostridium difficile, Geothrix fermentans, and the genus Thiobacillus were specific to the littoral bacteriobenthos community. The bacterial community of the pelagic zone was characterized by a change of dominant taxa in autumn. The increase of bacteriobenthos biomass and its particular taxa was significantly affected by the water temperature, redox potential, and the content of humic substances.