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Methane (CH 4 ), carbon dioxide (CO 2 ) and nitrous oxide (N 2 O) are known to be major greenhouse gases that contribute to global warming. To identify the flux dynamics of these greenhouse gases is, therefore, of great significance. In this paper, we conducted a comparative study on an alpine grassland and alpine wetland at the Bayinbuluk Grassland Eco-system Research Station, Chinese Academy of Sciences. By using opaque, static, manual stainless steel chambers and gas chromatography, we measured the fluxes of CH 4 , N 2 O and CO 2 from the grassland and wetland through an in situ monitoring study from May 2010 to October 2012. The mean flux rates of CH 4 , N 2 O and CO 2 for the experimental alpine wetland in the growing season (from May to October) were estimated at 322.4 μg/(m 2 •h), 16.7 μg/(m 2 •h) and 76.7 mg/(m 2 •h), respectively; and the values for the alpine grassland were -88.2 μg/(m 2 •h), 12.7 μg/(m 2 •h), 57.3 mg/(m 2 •h), respectively. The gas fluxes showed large seasonal and annual variations, suggesting weak fluxes in the non-growing season. The relationships between these gas fluxes and environmental factors were analyzed for the two alpine ecosystems. The results showed that air temperature, precipitation, soil temperature and soil moisture can greatly influence the fluxes of CH 4 , N 2 O and CO 2 , but the alpine grassland and alpine wetland showed different feedback mechanisms under the same climate and environmental conditions.