The fluxes of CO2 and CH4 emission of the two types of primary swamp were measured in Sanjiang Plain using the opaque chamber and gas chromatogram technique. The mean value of ecosystem respiration flux in continuously inundated swamp ecosystem is 548.04 mg·m-2·h-1, lower than that of the seasonal inundated swamp (713.08 mg·m-2·h-1). The peaks concentrated on July and August which are the growing period of the vegetation. CH4 emission was different from the respiration flux of ecosystem. The CH4 flux of continuously inundated swamp was 12.80 mg·m-2·h-1, larger than that of the seasonal inundated swamp (8.56 mg·m-2·h-1), and they were varied at different periods, the continuously inundated swamp emitted CH4 mainly from July to September, whereas from last August to middle September in the seasonal inundated swamp. The ecosystem respiration flux of the swamp has the significantly positive correlation with the soil temperature (0-10 cm depth) and the water temperature, but CH4 emission was associated with the soil temperature in a certain degree. The CH4 emission from swamp depends on the integral function of water table and soil temperature.