Surface sediments from the lower Yangtze River and the East China Sea (ECS) shelf were analyzed for the presence of bacteriohopanepolyols (BHPs), including three containing an NH2 group at C-35 (35-amino-BHPs). The three compounds are produced by aerobic methane oxidizing bacteria, with the hexafunctionalised 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being highly specific for Type I methanotrophs. The concentrations of these diagnostic compounds in surface sediments are compared with dissolved CH4 concentrations in the water column from the river-ECS system to validate the applicability of the molecular proxies and to identify focal points of methane cycling in the study area. The results show low 35-amino-BHP concentrations in riverbed sediments underlying waters with high CH4 concentrations, indicative of little CH4 oxidation in the river. Rapid removal of methane is, however, observed in the upper Yangtze Estuary and is clearly matched by a dramatic increase in 35-amino-BHP concentration in the surface sediments. Both observations strongly argue for enhanced aerobic methane oxidation and the potential of 35-amino-BHPs, and aminopentol in particular, as sensitive markers of this biogeochemical process. Further offshore, concentrations of sedimentary 35-amino-BHP and water column CH4 rapidly decrease seaward.