Artic permafrost environments play an important role within the global methane cycle. Thawing of permafrost and the associated release of this climate relevant trace gas, due to an increased microbial turnover of organic carbon and from ancient methane reservoirs, represent a potential risk to global warming. For the prediction of a future development of the permafrost environment and its contribution to the global atmospheric carbon budget, it is important to understand how this system reacted to environmental changes in the past. The Elgygytgyn lake region, Northeast Siberia, represents an ideal model system for studying the response of the methane cycle to climate change. It is supposed to be unglaciated since the time of a meteorite impact 3.6 Ma ago and since that time the permafrost went through four major climate-induced stages during the last 300,000 years. These changes in climate caused chemical and physical variations in sedimentary column and thus we expect changes in the composition of key microrganisms that were implicated in methane cycle. A 140 m long permafrost core from Elgygytgyn lake region was recovered within the ICDP project Scientific Drilling in Elgygytgyn Crater Lake in November 2008. Our studies will be conducted on combining microbial biomarker analyses and rRNA gene analyses in a high stratigraphic resolution. While rRNA gene sequences provide detailed informations on taxonomy, the extraction and analyses of microbial marker molecules are quantitative and correlate to cellular biomass. These two approaches are independent and thus can verify each others results. In addition to these studies, methane concentrations as well as the methane production and oxidation activity will be determined in the deposits. The obtained data will be interpreted in context of the results on inorganic properties in permafrost deposits of the Elgygytgyn lake region and paleoclimate reconstructions in this area provided by cooperation partners of the ICDP project Scientific Drilling at Elgygytgyn Crater Lake.