Objective Airborne microbial communities include a significant number of uncultured and poorly characterized bacteria. No effective method currently exists to evaluate the health risks of such complex bacterial populations, particularly for pneumonia. Methods We developed a method to evaluate risks from airborne microorganisms, guided by the principle that closer evolutionary relationships reflect similar biological characteristics, and thus used 16S rDNA sequences of 10 common pneumonia-related bacterial pathogens. We calculated a risk of breath-related (Rbr) index of airborne bacterial communities and verified effectiveness with artificial flora and a clinical project. Results We suggested applying Rbr80 to evaluate the health risks of airborne bacterial communities that comprise 80％ of dominant operational taxonomic units (OTUs). The feasibility of Rbr80 was confirmed by artificial flora and by pneumonia data from a hospital. A high Rbr80 value indicated a high risk of pneumonia from airborne bacterial communities. Conclusion Rbr80 is an effective index to evaluate the pneumonia-associated risk from airborne bacteria. Values of Rbr80 greater than 15.40 are considered high risk.