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The Arctic is exposed to even faster temperature changes than most other areas on Earth. Constantly increasing temperature will lead to thawing permafrost and changes in the methane (CH4) emissions from wetlands. One of the places exposed to those changes is the Abisko–Stordalen Mire in northern Sweden, where climate and vegetation studies have been conducted since the 1970s. In our study, we analyzed field-scale methane emissions measured by the eddy covariance method at Abisko–Stordalen Mire for 3 years (2014–2016). The site is a subarctic mire mosaic of palsas, thawing palsas, fully thawed fens, and open water bodies. A bimodal wind pattern prevalent at the site provides an ideal opportunity to measure mire patches with different permafrost status with one flux measurement system. The flux footprint for westerly winds was dominated by elevated palsa plateaus, while the footprint was almost equally distributed between palsas and thawing bog-like areas for easterly winds. As these patches are exposed to the same climatic and weather conditions, we analyzed the differences in the responses of their methane emission for environmental parameters. The methane fluxes followed a similar annual cycle over the 3 study years, with a gentle rise during spring and a decrease during autumn, without emission bursts at either end of the ice-free season. The peak emission during the ice-free season differed significantly for the two mire areas with different permafrost status: the palsa mire emitted 19 mg-C m−2 d−1 and the thawing wet sector 40 mg-C m−2 d−1. Factors controlling the methane emission were analyzed using generalized linear models. The main driver for methane fluxes was peat temperature for both wind sectors. Soil water content above the water table emerged as an explanatory variable for the 3 years for western sectors and the year 2016 in the eastern sector. The water table level showed a significant correlation with methane emission for the year 2016 as well. Gross primary production, however, did not show a significant correlation with methane emissions. Annual methane emissions were estimated based on four different gap-filing methods. The different methods generally resulted in very similar annual emissions. The mean annual emission based on all models was 3.1 ± 0.3 g-C m−2 a−1 for the western sector and 5.5 ± 0.5 g-C m−2 a−1 for the eastern sector. The average annual emissions, derived from these data and a footprint climatology, were 2.7 ± 0.5 and 8.2 ± 1.5 g-C m−2 a−1 for the palsa and thawing surfaces, respectively. Winter fluxes were relatively high, contributing 27 %–45 % to the annual emissions.