Methane is one of the main greenhouse gases and plays an important role in global climate change. Wetlands are the main source of global methane emission. Microbial communities inhabiting anoxic habitats such as freshwater wetlands and marine sediment are important for biological carbon cycling. Methanogenesis is the final step of degradation of organic substrates and mediated by methanogenic archaea. Rising sea levels and excessive water withdrawals upstream are making previously freshwater wetlands saline. Plant community responses to change in the freshwater-saline gradient have been well studied in the estuarine wetlands; however, microbial community structure response to salinity gradient remains relatively unexplored, including the methanogens in tidal marsh soil along salinity gradient in subtropical estuary are poorly characterized.It is essential to investigate the influence of salinity on the community structure of methanogen in tidal marshes. With the development of molecular biological techniques, molecular methods independent of culture techniques has vastly improved the potential to describe microbial diversity. Methyl-coenzyme M reductase is a critical enzyme in methanogenesis and the mcrA gene is a favorable functional gene and widely used to detect methanogens in soils of wetlands. Here, we determined the diversity of methanogen communities using molecular technique targeting the mcrA gene and restriction fragment length polymorphism (RFLP) from the soil of the tidal freshwater and brackish Cyperus malaccensis marshes in the Min River estuary, southeast China. The community structure of methanogen in the tidal C. malaccensis marshes changed with salinity. Values of Shannon-Weiner index of methanogen from the soil of tidal freshwater C. malaccensis marshes are 2.81 and 2.65 in the Xiayangzhou and Tajiaozhou wetlands, and 2.33 and 2.27 in the soil of tidal brackish C. malaccensis marshes in the Bianfuzhou and Shanyutan wetlands. The diversity of methanogen communities from the tidal C. malaccensis marshes decreased with increasing salinity in the Min River estuary. Phylogenetic analysis revealed that the communities of methanogens in the C. malaccensis marshes were mainly divided into three groups which were Methanomicrobiales, Methanosarcinales and Methanobacteriales. The freshwater C. malaccensis marshes were mainly dominated by Methanoregula,Methanosarcina and Methanobacterium.However, the brackish C. malaccensis marshes only dominated by Methanoregula. We conclude that methanogen diversity in estuarine tidal marshes is shaped by salinity conditions, suggesting an influence of impending sea level rise.