Emergent macrophytes are of key importance for the structure and functioning of wetland ecosystems and play a significant role in climate regulation, element cycling, and greenhouse gas emissions. However, our understanding of how greenhouse gas (GHG) flux differs among macrophyte species and its links with the microbial community remains limited. In this study, we investigated the rhizosphere microbial communities (including total bacteria, methanotrophs, and methanogens) and the GHG fluxes associated with four emergent macrophytes-Phragmites australis, Thalia dealbata, Pontederia cordata, and Zizania latifolia-collected from Xuanwu Lake wetland, China. We observed the highest CH4 flux (FCH4) (9.35 ± 2.52 mg·m-2·h-1) from Z. latifolia zone, followed by P. australis, P. cordata, and T. dealbata zones (5.38 ± 1.63, 2.38 ± 2.91, and 2.02 ± 0.69 mg·m-2·h-1, respectively). In zone without macrophyte growth, the CH4 flux was 0.02 ± 0.24 mg·m-2·h-1. Methanogenesis is methylotrophic at all sites, as the 13C-CH4 values were higher than -64 ‰ and the fractionation coefficient were lower than 1.055. We found a positive linear relationship between CH4 flux and the methanogen community, in particular the relative abundance of Methanobacterium and Methanosarcina, indicating that the variations in CH4 flux among the studied macrophyte species might be attributed to differences in rhizosphere microbial communities. The methane emission in various macrophyte zones may be due to the higher capacity of methanogenesis compared to methane oxidation which is inhibited by nutrient-rich sediments. Our findings provide insights for selecting specific emergent macrophytes characterized by low CH4 flux in wetland ecological restoration.