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Treatment Wetlands (TW) are very effective in the wastewater purification. Their biocenoses are capable to degrade various organic pollutants. However, not much is known about the selection of bacteriocenosis takes place in TW, and how the structure of such complex community reflects its functions, useful for water treatment. The aim of the study is to analyze composition of bacterial community in different zones of TW, detect all functional groups of bacteria and compare this data with results of chemical analysis. The object of study is Free Water Surface Constructed Wetland in Moscow, it receives stormwater and some industrial effluents. It is a flow reactor divided into 5 zones. The structure of bacteriocenosis in sludge and water, content of organic pollutants (polycyclic aromatic hydrocarbons, phthalates, surfactants) in different zones of TW were investigated. Sequencing of 16S rRNA was carried out on Illumina MiSeq. The pair-end reads were filtered and merged using MeFiT (https://github.com/nisheth/MeFiT) (Parikh et al., 2016). Taxonomy assignment of the OTU sequences up to genera level with adjustment for the gene copy number was performed using the RDP database (http://rdp.cme.msu.edu/) with the RDP classifier (Cole et al., 2014). Microbial diversity was estimated using the Shannon, Chao1, and abundance-based coverage indixes. Bray-Curtis dissimilarity was used to explore the variation in prokarytic community structures among all the samples. GC-MS (Agilent GC 6890 MSD 5970), HPLC (Agilent 1200) were used for chemical analysis. We have detected 17 genera of methanogens. The methanotrophic community was represented only by 4 genera. A total of 21 genus of methylotrophic microorganisms were detected. Phototrophic microorganisms were among the dominant in TW, especially in anaerobic sites. The most representative phototrophs were cyanobacteria, reached 20–25% of the total microbiome. Content of the sulfate-reducingmicroorganisms ranged from 0.5 to 3%. The patterns of distribution of the main phylogenetic groups of microorganisms, which are biologically active components of TW were identified. As a result, relationships between community structure and water treatment efficiency in each zone were determined. Zones with plants proved to be most effective in removing xenobiotics.