Permafrost environments are supposed to be strongly affected by the currently observed global temperature rise. About one third of global soil carbon is preserved in permafrost and an increase in temperature might increase the microbial turnover of recent as well as ancient carbon and cause the release of large amounts of greenhouse gases such as methane. To predict future methane emissions and to estimate the global atmospheric carbon budget, we need to understand the present composition of microorganisms being involved in cycling of methane and know their response to climate changes in the past. Therefore, a combination of quantitative and qualitative analyses of the variations in composition of bacterial and archaeal communities involved in the Siberian methane cycle was accomplished to reveal variations in permafrost deposits of the Holocene and Late Pleistocene. Such an approach was used on permafrost sediments for the first time.A 23 m long permafrost core drilled in 2002 on Kurungnakh Island, Lena Delta, Siberia, was examined using biogeochemical as well as microbiological methods. The interpretation of our data was done in context of a paleoclimate reconstruction based on pollen analysis at the same site (Schirrmeister et al., 2002). The sediments of Kurungnakh achieve different climatic stages: cold & dry, warm & wet, Holocene warming. As a general result it is shown that it was possible to recover lipid biomarkers and amplifiable DNA throughout the Kurungnakh permafrost sequence with an age of up to 42 ka. First analyses of glycerol dialkyl glycerol tetraethers (GDGTs) were conducted. GDGTs provide paleo-signals of archaeal and bacterial communities, since these lipids are already partly degraded but their core lipids are relatively stable outside intact cells. Highest amounts of ether lipids were found in the upper layer and at the bottom of the core. Total GDGT contents show highest concentrations with 495 ng/g sediment at 122 cm depth, with 70 ng/g sediment at 1184 to 1745 cm and with about 400 ng/g sediment at 2320 cm depth, whereas GTGTs are dominated by bacterial branched GDGTs. Generally, the results of GDGT analyses correlate to measured contents of total organic carbon (TOC) and concentrations of in-situ methane in the deposits. Furthermore vertical variations of archaeal biomarkers such as archaeol, caldarchaeol and crenarchaeol could be detected. Archaeol concentration varied between 3.84 and 62.5 ng/g sediment. The highest amounts were measured on top and bottom of the core and at a peak at 1745 cm depth. These changes are probably caused by changing compositions of archaeal communities as a response to temperature changes.To complete our information on the qualitative composition of microbial communities, DNA-based analyses using DGGE and clone libraries were conducted using archaeal and methanotrophic specific primer combinations. Fingerprints of archaeal 16 S rRNA gene sequences of the different permafrost samples show distinct variations in the microbial community composition within the vertical profile. Sequence analyses showed a diversity of methanogens affiliated with Methanobacteriaceae, Methanosarcinaceae and Methano-microbiaceae. Highest diversity of methanogens could be detected at depth of 1507 cm and 1745 cm, which were also characterized by high amounts of archaeol, whereas samples with a low amount of archaeol showed only less diversity.Additionally the presence of aerobic methanotrophic communities was analysed using diploptene (Hop-22(29)ene) as a characteristic biomarker. We suggest that this marker reflects fossil communities of methane oxidizing bacteria being present during time of sedimentation of the respective deposits (former upper aerobic active layer). The variability of the diploptene distribution correlates to measured rates of methane and content of TOC. The presence of high amounts of diploptene might be caused by the release of considerable amounts of methane being substrate to the aerobic methanotrophic communities in former active layer. This process is stimulated by temperature since content of diploptene increases with warming events. We suggest that paleo methane emissions from permafrost appear to be higher during warmer periods.Both biogeochemical as well as microbiological methods revealed variation within the composition of past and present microbial communities and showed indications of response to climate changes.