Dust deposition is considered an important source of many bioavailable nutrients to the marine environment. Nutritional status is the main factor regulating bacterioplankton growth, and thus it is important to study the effects of dust deposition. Microcosm experiments with dust aerosol addition were performed using surface water from the South China Sea (SC) for 12 days and southern Yellow Sea (SY) for 10 days. After incubation, the bacterial biomass in microcosms increased 10.82-fold and 2.22–3.32-fold under dust addition, in SC and SY respectively. Bacterial growth was also stimulated by dust aerosol, indicated by increased and more effcient heterotrophic secondary production. In addition, bacterial community structures were simplified by dust aerosol in both study areas. Alpha- and gamma-proteobacteria were the predominant bacteria in the microcosms following dust addition in SC, whereas alpha- and delta-proteobacteria were the main bacteria in SY. These results demonstrate that dust deposition regulates growth and community structure of marine bacteria in SC and SY by promoting phytoplankton growth.