To evaluate the effect of vegetation change on greenhouse gas (GHG) budget from a wetland ecosystem, the CO2, CH4 and N2O budgets from whole area (21.5 ha) of the Bibai Wetland, where dwarf bamboo (Sasa) or Ilex has invaded into original Sphagnum dominated vegetation, located in Hokkaido, Japan were estimated. The original Sphagnum-dominated vegetation was changed from a sink to a source of CO2 by invasion of short-Sasa (50 cm > height), while the invasion of tall-Sasa (50 cm < height < 150 cm) or Ilex increased CO2 uptake. Annual CH4 emission was decreased by the invasion of Sasa or Ilex. The annual N2O emission was slightly increased by invasion of Ilex only. These GHG budgets were correlated with the environmental factors related to the water table depth. The distribution of vegetation and environmental factors was estimated from satellite image bands, and the GHG budget of the entire wetland was estimated. The whole wetland area was considered to be a sink for GHG (-113 Mg CO2-eq y(-1)) and CO2 uptake by tall-Sasa occupied 71% of the GHG budget. The vegetation change due to the lowering of the water table depth currently increases the rate of carbon accumulation in the ecosystem by about 5 times.