Arctic tundra ecosystems have been major carbon sinks throughout the Holocene. However, during the past decades the Arctic has been observed to warm faster than lower latitudes in the context of global climate change. Large uncertainties about the actual and consequently also the future contribution of these environments to the global carbon cycle remain especially with regard to methane emissions. In order to address this uncertainty, landscape-scale measurements as well as investigations of the small-scale variability of methane emission are necessary in different arctic ecosystems. Eddy covariance measurements of methane flux were carried out in northern Siberian wet polygonal tundra during 41 days in July/August of 2005 and during 122 days covering the entire growing season in 2006. Additionally, closed chamber measurements of methane fluxes were conducted daily at 15 plots in four different types of depressed polygon centres and a polygon wall during August 2005 and from July through September in 2006. Floating chambers were used to investigate the contribution of water-filled cracks and thermokarst lakes. The study site is the only eddy correlation and chamber methane flux measurement site in arctic Siberia and was located in the zone of continuous permafrost in the southern part of the Lena River Delta (72°N, 126°E). We present the landscape scale methane budget for the 2006 growing season as determined by the eddy correlation method and the identified control mechanisms of methane emission at the wet polygonal tundra site. For comparison of the different spatial scales, we also present results of our closed chamber methane flux measurements within the eddy covariance measurement footprint demonstrating the great small-scale variability of methane emission at polygonal tundra.