PurposeAlpine wetland ecosystems can contribute large amounts of methane (CH4) to the atmosphere; however, their emissions vary with environmental conditions. Microbial activity is known to drive CH4 emissions, but how environmental conditions determine microbial activity is still uncertain. Here, we seek to quantify the variability of the CH4 flux, to detect the effects of CH4-related microbes on CH4 emissions, and to study the dependency of these effects on environmental conditions.Materials and methodsWe measured the CH4 flux, environmental conditions, and CH4-related microbial communities (mcrA and pmoA gene abundances for methanogens and methanotrophs, respectively) under three hydrological conditions (submerged, soil–water interface, and emerged) from seven sampling sites in the Zoige alpine wetland, China.Results and discussionThe CH4 flux varied greatly from 0 to 41 mg m−2 h−1 in the Zoige alpine wetland. The methanogenic and methanotrophic abundances both showed positive correlations with CH4 flux, while CH4 flux increased linearly with the increase of soil water content (SWC) when SWC was above 60%. CH4 flux and methanogenic and methanotrophic abundances maintained the high levels when soil C:N ratio was in the range of 11–24 and decreased exponentially with the increase of soil DOC:TN ratio in Zoige alpine wetland, which might result from its influence on nutrient supply for microbial decomposition process.ConclusionThe results provided new insight into the effects of CH4-related microbes on CH4 emission and its response to different environmental conditions and helped us to comprehend the risks of high CH4 emissions from alpine wetlands under climatic change and anthropogenic disturbance.