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Methane fluxes, which are controlled by methanogens and methanotrophs, vary among wetland vegetation species. In this study, we investigated belowground methanogens and methanotrophs in two soils under two different dominant vegetation species with different methane fluxes in the Zoige wetland, which was slightly but significantly (p <= 0.05) higher in soils covered by Carex muliensis than that in soils covered by Eleocharis valleculosa. Real-time quantitative PCR and Illumina MiSeq sequencing methods were used to elucidate the microbial communities based on the key genes involved in methane production and oxidation. The absolute abundances of methanogens and methanotrophs of samples from C. muliensis were 1.80 +/- 0.07 x 10(6) and 4.03 +/- 0.28 x 10(6) copies g-soil(-1), respectively, and which from E. valleculosa were 3.99 +/- 0.19 x 10(5) and 2.53 +/- 0.22 x 10(6) copies g-soil(-1) , respectively. The t-test result showed that both the abundance of methanogens and methanotrophs from C. muliensis were significantly higher (p <= 0.05) than that of samples from E. valleculosa. However, the diversities and compositions of both methanogens and methanotrophs showed no significant differences (p >= 0.05) between vegetation species. The path analysis showed that the microbial abundance had a greater effect than the microbial diversity on methane production potentials and the regression analysis also showed that the methane emissions significantly (p <= 0.05) varied with the abundance of methane-cycling microbes. These findings imply that abundance rather than diversity and composition of a methane-cycling microbial community is the major contributor to the variations in methane emissions between vegetation types in the Zoige wetland.