This study compares the CH<sub>4</sub> fluxes from two arctic wetland sites of different annual temperatures during 2004 to 2006. The PEATLAND-VU model was used to simulate the emissions. The CH<sub>4</sub> module of PEATLAND-VU is based on the Walter-Heimann model. The first site is located in northeast Siberia, Indigirka lowlands, Kytalyk reserve (70° N, 147° E) in a continuous permafrost region with mean annual temperatures of −14.3°C. The other site is Stordalen mire in the eastern part of Lake Torneträsk (68° N, 19° E) ten kilometres east of Abisko, northern Sweden. It is located in a discontinuous permafrost region. Stordalen has a sub arctic climate with a mean annual temperature of −0.7°C. Model input consisted of observed temperature, precipitation and snow cover data. <br><br> In all cases, modelled CH<sub>4</sub> emissions show a direct correlation between variations in water table and soil temperature variations. The differences in CH<sub>4</sub> emissions between the two sites are caused by different climate, hydrology, soil physical properties, vegetation type and NPP. <br><br> For Kytalyk the simulated CH<sub>4</sub> fluxes show similar trends during the growing season, having average values for 2004 to 2006 between 1.29–2.09 mg CH<sub>4</sub> m<sup>−2</sup> hr<sup>−1</sup>. At Stordalen the simulated fluxes show a slightly lower average value for the same years (3.52 mg CH<sub>4</sub> m<sup>−2</sup> hr<sup>−1</sup>) than the observed 4.7 mg CH<sub>4</sub> m<sup>−2</sup> hr<sup>−1</sup>. The effect of the longer growing season at Stordalen is simulated correctly. <br><br> Our study shows that modelling of arctic CH<sub>4</sub> fluxes is improved by adding a relatively simple hydrological model that simulates the water table position from generic weather data. Our results support the generalization in literature that CH<sub>4</sub> fluxes in northern wetland are regulated more tightly by water table than temperature. Furthermore, parameter uncertainty at site level in wetland CH<sub>4</sub> process models is an important factor in large scale modelling of CH<sub>4</sub> fluxes.