Abstract: In this study, we investigated the impacts of submerged macrophytes rehabilitation(SMR) on the methanogenic community structure in the lake sediments. We compared the diversity and structure of methanogenic populations between the SMR areas and the plant scarce areas in the West Lake of Hangzhou by using restriction fragment length polymorphism(PCR-RFLP) and molecular cloning techniques. The results showed that the average OTU type number in the SMR areas was 13, and the number was 9 in the scarce areas. Shannon-Weaver diversity and Simpson's evenness in the SMR areas were 21.7% and 9.5% respectively, which were higher than those in the control areas. This indicated that the diversity of the methanogenic community structure could be improved by the rehabilitation of submerged macrophytes. The in-depth analysis suggested that SMR had no significant effect on Methanomicrobia that accounted for 43.6%-67.4% and 41.5%-58.1% in the SMR areas and the scarce areas respectively. Methanococci was rare in both the SMR areas(1.7%) and the scarce areas(4.1%). We also found that the proportion of Methanobacteria in the SMR areas was 14.6% higher than in the scarce areas. Methanothermaceae and Methanosarcinaceae were only detected in the SMR areas.