Abstract: The biomass distribution characteristics of total bacteria, aerobic ammonium-oxidizing and denitrifying bacteria in sediments from Changjiang Estuary and adjacent sea area were analyzed using DAPI staining and fluorescent quantitative PCR technology. For the vertical distribution, denitrifying bacteria (DB) biomass was much higher than that of aerobic ammonium-oxidizing bacteria (AOB) at the same depth, but there were similar trends between their vertical biomass. The intense mixing of sediments was suitable for AOB coexisting with DB. Sediment depth was the most significant influencing factor to the vertical biomass profiles of total bacteria, AOB and DB. The increasing depth affected AOB more easily than total bacteria and DB. For the horizontal distribution, total bacterial biomass gradually decreased from inshore to offshore, which was significantly impacted by the nitrite concentration. There were high biomass areas of AOB and DB in the sea area off Changjiang Estuary and the south sea area of Zhoushan Archipelago, respectively, and dissolved oxygen concentration and total nitrogen content were important influencing factors to their horizontal distributions. This study provided support for thoroughly understanding the role of bacteria in nitrogen cycles in estuarine and coastal sea area.