Wetlands at the interface of the terrestrial and aquatic ecosystems are intensive sites for mineralization of organic matter,but the contribution of winter season fluxes of CH4, CO2 and N2O from wetland ecosystems to annual budgets is poorly known. By using the static opaque chamber and GC techniques, fluxes of CH4, CO2 and N2O at two freshwater marshes in the Sanjiang Plain were measured during the winter seasons of 2002/2003 and 2003/2004 with contrasting snow conditions and flooding regimes. The results showed that there were significant interannual and spatial differences in CH4, CO2 and N2O fluxes. The Carex lasiocarpa marsh emitted more CH4 and CO2 while absorbed less N2O than the Deyeuxia angustifolia marsh during the winter seasons. Over the winter season,emissions of CH4, CO2 and N2O ranged from 0.42 to 2.41 gC/m2, from 24.13 to 50.16 gC/m2, and from -25.20 to -148.96 mgN/m2,respectively. The contributions of winter season CH4 and CO2 emission to the annual budgets were 2.32%-4.62% and 22.17%-27.97%, respectively. Marshes uptake N2O during the freezing period, while release N2O during the thawing period. The winter uptake equaled to 13.70%-86.69% of the growing-season loss. We conclude that gas exchange between soil/snow and the atmosphere in the winter season contributed greatly to the annual budgets and cannot be ignored in a cool temperate freshwater marsh in Northeast China.