Cyanobacteria Anabaena and Microcystis containing microcystin synthesis genes were found for the first time in the littoral zone of Lake Baikal near Turka village. Microcystin concentration in water according enzyme-linked immunosorbent assay (ELISA) was 0,17±0,01 mg /l. Genetic and taxonomic composition of microbial community in Central Baikal was characterized by using pyrosequencing, 3936 nucleotide sequences of 16S rRNA gene fragment were identified. The phylum Cyanobacteria was dominant in the summer bacterioplankton of the littoral and pelagic zones, whereas higher biodiversity was recorded in the littoral plankton.