Methane is the second important greenhouse gas after carbon dioxide. Seagrass meadows colonized along the coastline are significant net methane sources. Methanogenesis is the terminal step of organic carbon degradation in marine sediments.There are three main methanogenesis pathways: hydrogenotrophic, aceticlastic and methylotrophic. Hydrogenotrophic methanogens utilize hydrogen as electron donors to reduce carbon dioxide. Acetate is activated to acetyl-CoA, then reduced to methane through the aceticlastic methanogenesis. Methylotrophic methanogens have substrate-specific methyltransferase systems, which can reduce three quarters of the methyl groups to methane and oxidize one quarter to carbon dioxide. In marine sediments, where sulfate is abundant, hydrogenotrophic and acetoclastic methanogenesis are usually inhibited because of the competition for hydrogen and acetate with sulfate-reducing bacteria. Thus, methylotrophic methanogenesis is crucially important. To evaluate the relative importance of the three methanogenesis pathways in seagrass meadows, we collected four sediment cores located in Cymodocea nodosa, Enhalus acoroides, Thalassia hemperichii and bare sediment, respectively, and did metagenome analysis. The relative abundances of the relevant genes were evaluated. Three metabolic pathways were identified in the seagrass meadows. And methanogenesis pathways in different seagrass species sediments were compared.