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Methane emissions from wetlands contribute to the currently rising levels of methane in the atmosphere. Nonetheless, the assessments of methane-producing Archaea (methanogens) and their environmental controls are still rare particularly in soils from estuarine tidal marshes. In estuarine tidal marshes, the salinity gradient is commonly observed, and its effects on the methanogenic community are hardly known. In this study, in the Min River estuary, southeast China, we analyzed two freshwater and two brackish (oligohaline) marshes in a subtropical estuary, where we assessed methanogenic community structure and abundance by molecular cloning, sequencing, and quantitative PCR methods, as well as by means of soil physicochemical characteristics and concentration of methane dissolved in pore water. The common and dominant genera of these methanogens include Methanoregula , Methanobacterium , Methanosarcina , and Methanolinea in the four marshes. Phylotypes of the methanogens using H 2 /CO 2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in the mcrA gene clone libraries and by restriction fragment length polymorphism (RFLP) analyses. The abundance levels of methanogens in the two freshwater marshes were significantly higher than those in the two brackish marshes. The value of the Shannon Index ( H ′) of diversity and Simpson index ( D ) of evenness of methanogen mcrA clone libraries decreased along the salinity gradient from freshwater to brackish water. Methanogen community structure varied with soil depth in the four wetlands. The concentrations of methane in pore water also decreased from the freshwater sites to the brackish sites; this pattern is consistent with a change in the abundance of methanogens. Our results showed that in a low-level salinity gradient of a subtropical estuary, salinity is still a major factor controlling the overall community structure and abundance of methanogens. [ABSTRACT FROM AUTHOR]