Introduction: Submarine arctic permafrost was formed when sea level rise flooded terrestrial permafrost and warmed the frozen sediments during the Holocene. This thawing permafrost may play a major role in global warming as it stores huge amounts of organic carbon. Hitherto, the extent and importance of microbial activity on carbon transformations as well as the reactions of microorganisms to the environmental changes accompanying the inundation of permafrost by sea water are poorly understood. Objectives: We investigated the impact of sea level rise on methane cycle associated microbial communities in degrading permafrost of the western and central Laptev Sea shelf, Siberian. Material and methods: Two sediment cores were retrieved (77 m and 52 m deep) from the coastal shelf north of Cape Mamontov Klyk ‘C2’ (11.5 km offshore) and west of Buor Khaya Peninsula ‘BK2’ (800 m offshore), respectively. Chemical parameters such as total organic carbon (TOC), methane concentrations and 13 C isotope values were measured and correlated with molecular analysis of microbial communities along the cores. Results: Frozen sediment was encountered at 35.5 (C2) and 28 (BK2) meters below sea level (mbsl), respectively. Methane concentrations varied between 0.21 and 284.31 nmol g-1with highest values in the frozen permafrost and lowest values in the overlaying unfrozen sediments. Low methane concentrations in the unfrozen sediments of BK2 (16.25-28.20 mbsl) correlated with the highest carbon isotope values of methane (-29.8 ‰ VPDB) indicating microbial oxidation of methane under in situ conditions in the thawing permafrost. Bacterial cell numbers (16S rRNA) and functional genes (mcrA) of methanogenic archaea and sulphate reducing bacteria (dsrB) analysed by quantitative PCR often peaked at high methane or TOC concentrations in the frozen permafrost and showed specific 13CH4isotopic values indicating distinct methanogenic populations. Conclusion : Our data give first insights into how the inundation of permafrost by sea water influences the abundance of active members of the microbial methane cycle both along thawed and still frozen sediments. Further analysis of amplicon sequencing and quantitative analysis by fluorescence in situ,hybridization will give a better overview of these highly dynamic microbial populations.