Bioaerosols are biological aerosols which contain microorganisms such as fungi, spores, bacteria, virus, and pollens. Bioaerosols should be considered an important factor which affects air quality, atmosphere of natural environment, and human health. At present, there are few reports for infectious risk management of bioaerosols (number concentration of microorganisms, organism species etc.), the role of bioaerosols in the ecosystem and the effect of bioaerosols on climate. In fact, it's difficult to investigate the total microorganisms in bioaerosols by culture-based method, because 99 % of bacteria in almost every environment on earth is unable to be detected and analyzed under laboratory conditions. As a method to overcome this bottleneck, a metagenomic analysis method for unculturable microorganisms in bioaerosols was described in this report.