Sediments of Håkon Mosby Mud Volcano (HMMV) are characterized by different microbial communities, which are oxidizing methane that is advectively transported to the sediment surface. Combined molecular and geochemical data reveal the presence of anaerobic oxidation of methane (AOM) in Beggiatoa and Pogonophera sediment areas whereas aerobic oxidation of methane is observed in the thermal center of HMMV. The activity is limited in each case to a narrow subsurface sediment horizon whereas the deeper layers are mostly inactive. Evidence for AOM is provided by lipid biomarker and fluorescence in situ hybridization (FISH) analyses, targeting microbial consortia of sulfate-reducing bacteria and methanotrophic archaea. The archaea detected could be assigned to a new group affiliated with Methanosarcinales, which is distinct from known phylogenetic groups involved in AOM (i.e., ANME1, ANME2). Comparative analyses show a correlating vertical distribution pattern with a sharp decline of sulfate concentration, biomarker concentration, aggregate number and AOM rate. A similar biogeochemical scenario is observed at the thermal center where, in contrast, aerobic methanotrophic gamma-proteobacteria dominate the microbial community. Biomarker analyses suggest that these bacteria are close relatives of known Methylomonas species. Without the processes of methane oxidation, the emission of methane to the hydrosphere would be even greater. Thus, the activity of the various microbial communities is an effective biological filter for methane seepage at HMMV.