The currently observed climate change due to global warming is expected to have a strong impact especially on the Arctic permafrost environments. The thawing of permafrost is suggested to be associated with a massive release of greenhouse gases, in particular methane. For the understanding how the system will respond to climate changes it is not only important to investigate the current status of carbon turnover but also how the system reacted to climate changes in the past. Therefore quantitative and qualitative analyses of the variations in composition of bacterial and archaeal communities involved in the Siberian methane cycle in holocene and late pleistocene were conducted, using samples of a permafrost core drilled in central Lena-Delta, Siberia, in 2002. Our studies on the reconstruction of the methane cycle in deposits of the permafrost affected soils combined methods of biogeochemistry and molecular geomicrobiology. It was possible to recover lipid biomarker and intact DNA continuously throughout the core. Biomarkers like glycerol dialkyl glycerol tetraethers (GDGTs) were analyzed whereas highest amounts of ether lipids were found in the upper layer and at the bottom of the core. Generally, the results of GDGTs analyzes fit to measured rates of total organic carbon (TOC) and in-situ methane concentration of the deposits. Furthermore these biomarkers were analyzed and distinguished in biomarkers representing signals of paleo-archaeal and paleo-bacterial communities. To complete information on the qualitative composition of microbial communities DNA analyses were driven using archaeal and methanotrophic specific primer combinations, whereas amplicons were subsequently analyzed by DGGE and clone libraries. Fingerprints of archaeal 16 S rRNA gene sequences of the different soil samples show variations within the vertical profile.