Abstract Comparing of different CH4 flux measurement techniques allows for the independent evaluation of the performance and reliability of those techniques. We compared three approaches, the traditional discrete Manual Static Chamber (MSC), Continuous Automated Chamber (CAC) and Eddy Covariance (EC) methods of measuring the CH4 fluxes in an alpine wetland. We found a good agreement among the three methods in the seasonal CH4 flux patterns, but the diurnal patterns from both the CAC and EC methods differed. While the diurnal CH4 flux variation from the CAC method was positively correlated with the soil temperature, the diurnal variation from the EC method was closely correlated with the solar radiation and net CO2 fluxes during the daytime but was correlated with the soil temperature at nighttime. The MSC method showed 25.3% and 7.6% greater CH4 fluxes than the CAC and EC methods when measured between 09:00 h and 12:00 h, respectively.