Natural wetlands and anthropogenic paddy fields are the dominant biogenic sources of atmospheric methane emission which have been speculated as the most probable sources for the increase of post-2006 atmospheric methane. Regional differences in CH4 emission is possibly due to microbial biogeographic distribution. Here we collected soils from 19 wetlands from different regions in China. The methane production capacity (MPC) was measured for each soil samples and varied from 1.11 to 841.94mg/kg dry soil. High throughput sequencing was employed to investigate the diversity and composition of bacterial, archaeal and methanogenic communities. Similar biogeographic patterns for bacterial, archaeal and methanogenic communities along the latitudinal gradient were observed, and the biogeographic assemblies of different microbial groups were driven by concurrent factors, including edaphic variables (total organic carbon, total phosphorus and pH) and climatic variables (annual frost days, mean annual temperature, direct solar radiation and mean annual precipitation). MPC was significantly correlated with TOC concentration, and in addition, various functional taxa were positively correlated with MPC (P<0.05), for example, Sphingomonas, Syntrophomonas, Methanospirillum and Methanoregula, indicating their potential contributions in the methanogenic process, and many of them were fermentative bacteria and methanogens. Network analysis showed that some syntrophs, sulfate-reducers and methanogens were tightly co-occurred in one module, suggesting their involvements in cross-linked functional processes. Our study implicated both temperature and substrate availability altered the biogeographic patterns of microbial community as well as methane production potential in Chinese wetlands.