For the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH4 production and oxidation, the community structure and the quality of DOM were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for esterlinked PLFAs and differences in the fraction of unsaponifiable PLFAs and PLELs. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso- and anteiso-branched fatty acids related to the amount of straight chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown, that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings firstly that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems. And secondly that these microorganisms are well adapted to the extreme temperature gradient of their environment.