The effect of microrelief and vegetation on methane (CH4) emission was investigated in a wet polygonal tundra of the Lena Delta, Northern Siberia (72.37N, 126.47E). Total and plant-mediated CH4 fluxes were measured by closed-chamber techniques at two typical sites within a low-centred polygon. During the study period, total CH4 flux averaged 28.0 ± 5.4 mg m−2 d−1 in the depressed polygon centre and only 4.3 ± 0.8 mg m−2 d−1 at the elevated polygon rim. This substantial small-scale spatial variability of CH4 emission was caused by strong differences of hydrologic conditions within the microrelief of the polygon, which affected aeration status and organic matter content of the soils as well as the vegetation cover. Beside water table position, the vegetation cover was a major factor controlling CH4 emission from polygonal tundra. It was shown that the dominant vascular plant of the study area, Carex aquatilis, possesses large aerenchyma, which serve as pathways for substantial plant-mediated CH4 transport. The importance of plant-mediated CH4 flux was strongly influenced by the position of the water table relative to the main root horizon. Plant-mediated CH4 transport accounted for about two-thirds of the total flux in the wet polygon centre and for less than one-third of the total flux at the moist polygon rim. A clipping experiment and microscopic-anatomical studies suggested that plant-mediated CH4 transport via C. aquatilis plants is driven only by diffusion and is limited by the high diffusion resistance of the dense root exodermes.