Airborne bacteria play key roles in terrestrial and marine ecosystems and human health, yet our understanding of bacterial communities and their response to the environmental variables lags significantly behind that of other components of PM2.5 Here, atmospheric fine particles obtained from urban and suburb Shanghai were analyzed by using the qPCR and Illumina Miseq sequencing. The bacteria with an average concentration of 2.12 × 103 cells/m3, were dominated by Sphingomonas, Curvibacter, Acinetobacter, Bradyrhizobium, Methylobacterium, Halomonas, Aliihoeflea, and Phyllobacterium, which were related to the nitrogen, carbon, sulfur cycling and human health risk. Our results provide a global survey of bacterial community across urban, suburb, and high-altitude sites. In Shanghai (China), urban PM2.5 harbour more diverse and dynamic bacterial populations than that in the suburb. The structural equation model explained about 27%, 41%, and 20%–78% of the variance found in bacteria diversity, concentration, and discrepant genera among urban and suburb sites. This work furthered the knowledge of diverse bacteria in a coastal Megacity in the Yangtze river delta and emphasized the potential impact of environmental variables on bacterial community structure.