Abstract: Mostly, the global methane emission comes from the metabolic activities of methanogens, which occurs in anaerobic environment. Based on the samples collected from typical stations in the Bohai Sea, we measured the concentrations of methane and sulfate in the sediments. The methane concentration in each sample was analyzed with different methanogenic substrates cultivation. The methanogen communities were measured by high-throughput sequencing techniques. The results indicated that the mainly methylotrophic pathway is methylotrophic methanogenesis, along with the hydrogenotrophic methanogenesis. Methane production decreased gradually with the depth increasing at the same station, and methane production rate decreased correspondingly at the same time. The archaea communities were dominated by Crenarchaeota, Asgardaeota and Nanoarchaeota, and Ca. Methanofastidiosales was the dominated methanogens. The results provide useful information for understanding the methanogenesis of methanogens in marine ecosystem.