A molecular analysis of natural cyanobacterial communities on travertine platforms of carbonated springs Zhoygan (East Sayan mountains) was carried out. The phylum of bacteria: Cyanobacteria, Verrucomicrobia, Proteobacteria, Chloroflexi and archaeans Euryarchaeota were identified. The analysis of clone library of has shown the prevalence of the bacterial domain.Cyanobacteria are dominant (35 %), and representatives of the class δ-Proteobacteria mainly determined among the Proteobacteria (17 %). Analysis of the functional characteristics of dominant genotypes microorganisms in bacterial mats showed that they carry out the processes of oxygenic and anoxic photosynthesis, destruction of organic matter, both aerobic and anaerobic conditions, and possess chemolithotrophic metabolism.