The observation of CH4 fluxes was performed in the Carex schmidtii marsh and Betula ovalifolia-Carex schmidtii shrub swamp ecosystems of Xiaoxing′an Mountains in the growing seasons of 2007 and 2008, using a static chamber and gas chromatography, to study the seasonal and inter-annual variations of CH4 flux and its relationships to environmental factors. The results showed that annual CH4 emissions from Carex schmidtii marsh and Betula ovalifolia-Carex schmidtii shrub swamp were, respectively, 66.60 and 3.20 kg?hm-2 in 2007 and 1482.60 and 18.15 kg?hm-2 in 2008. There was an obvious seasonal changes in CH4 emissions during the whole observation period, with the largest emissions in summer or in summer and fall for both years (1.88 and 0.092 mg?CH4?m-2?h-1 for the marsh and shrub swamp in 2007 and 34.18 and 0.43 mg?CH4?m-2?h-1 in 2008). There were significant differences of CH4 emissions between types of ecosystems and inter-annual changes. The seasonal variations of CH4 fluxes from both ecosystems were mainly associated with temperature, there were positive or negative relationships between CH4 fluxes and temperatures (air temperature, temperature inside the chamber, surface temperature and soil temperature of 0, 5,10,15, 20, 30, 40 cm ) in 2007 and they were positively related in 2008. Water table was one of main indicators which can affect seasonal and inter-annual changes in CH4 fluxes from the marsh and shrub swamps.