| Summary: | Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the <i>Acidobacteria</i> (30%–40% of total 16S rRNA gene reads), which belong to the orders <i>Acidobacteriales</i> and <i>Bryobacterales</i>. Other bog-specific bacteria included the <i>Phycisphaera</i>-like group WD2101 and the families <i>Isosphaeraceae</i> and <i>Gemmataceae</i> of the <i>Planctomycetes</i>, orders <i>Opitutales</i> and <i>Pedosphaerales</i> of the <i>Verrucomicrobia</i> and a particular group of alphaproteobacteria within the <i>Rhizobiales</i>. In contrast, fens hosted <i>Anaerolineae</i>-affiliated <i>Chloroflexi</i>, <i>Vicinamibacteria</i>- and <i>Blastocatellia</i>-affiliated <i>Acidobacteria</i>, <i>Rokubacteria</i>, uncultivated group OM190 of the <i>Planctomycetes</i> and several groups of betaproteobacteria. The <i>Patescibacteria</i> were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.
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