Permafrost-affected soils in the Arctic have been accumulating organic matter for thousands of years and form a carbon storage of global relevance. Large fractions of this carbon pool may, however, be remobilized in the form of the greenhouse gases CO2 and CH4 through the effects of Arctic warming and permafrost degradation. Within several Russian-German cooperation projects, we have been investigating the inter-annual variability of CO2 and CH4 exchange fluxes of lowland polygonal tundra on Samoylov Island in the Lena River Delta in the Siberian Arctic (72°N, 126°E) with the eddy covariance technique. The 16-year flux dataset from the polygonal tundra shows that this ecosystem is still a robust carbon sink. Cumulative net ecosystem CO2 exchange flux (NEE) during the late summer overlap period (15 July to 31 August) is rather consistent with -1.5 ± 0.6 mol m-2 (n = 15). The relationship between soil temperature and late summer NEE could be best fitted with a quadratic function (r2 = 0.44), which suggests the existence of a temperature optimum, where the difference between photosynthesis and ecosystem respiration leads to maximum net CO2 uptake. Probably, both photosynthesis and ecosystem respiration initially benefit from higher temperatures. In the highest temperature range, however, ecosystem respiration exceeds photosynthesis. Median CH4 fluxes during late summer ranged between 30 and 56 µmol m-2 hr-1 and were positively linearly correlated (r2 = 0.79, n = 11) with soil temperature at 7 cm depth in wet polygon centers. This result suggests that the enhancement of CH4 production by higher soil temperatures dominates over the enhancement of CH4 oxidation by higher soil temperatures in the studied polygonal tundra ecosystem. A longer and warmer thaw period may allow for a stronger accumulation of CH4 in soil pore space by methanogens and thus enhance transport processes which bypass oxidation (ebullition, plant-mediated transport).