Water ecosystems of Arctic region are most vulnerable to modern climatic changes, since global biogeochemical processes mostly occur on territories of permafrost zone. This work gives new insights into fundamental research question of how fast organic matter of thawing permafrost can be converted to greenhouse gases which are emitted into the atmosphere (for example, CH4). We aimed to identify microbial response and associated release of CH4 from Arctic lakes in response to temperature increase. We investigated lakes located in the Lena River delta on the Samoylov Island, Russia, at 72°22’N, 126°28’E. Bottom sediments from three thermokarst and three oxbow lakes were anaerobically incubated in laboratory at two temperature regimes (at 4 °C and at 25 °C). We identified different metabolic pathways of methane formation in thermokarst and oxbow lakes using the analysis of carbon isotopic composition in methane during the incubation period. Temperature increase caused methane emission from sediments of all of the lake types to rise. Our results suggest that in case of the global warming both thermokarst and oxbow lakes could become a great source of methane into the atmosphere.