Microbial diversity and abundance in bioaerosols of a coal mine were analyzed based on 454 pyrosequencing and real-time polymerase chain reaction(PCR). A total of 37,191 high quality sequences were obtained and could be classified into 531, 1730 and 448 operational taxonomic units respectively for archaea, bacteria and fungi at 97% sequence similarity. The Shannon diversity index for archaea, bacteria and fungi was respectively 4.71, 6.29 and 3.86, indicating a high diversity in coal mine bioaerosols. Crenarchaeota, Proteobacteria and Ascomycota were the dominant phyla for archaea, bacteria and fungi, respectively. The concentrations of total archaea, bacteria and fungi were 1.44 × 108, 1.02 × 108 and 9.60 × 104cells/m3, respectively.Methanotrophs observed in bioaerosols suggested possible methane oxidation in the coal mine. The identified potential pathogens to coal miners, such as Acinetobacter schindleri,Aeromonas cavernicola, Alternaria alternata, Aspergillus penicillioides, Cladosporium cladosporioides,and Penicillium brevicompactum were also observed. This was the first investigation of microbial diversity and abundance in coal mine bioaerosols. The investigation of microbial communities would be favorable in promoting the progress of methane control based on microbial technique and concern on coal miners’ health. Microbial diversity and abundance in bioaerosols of a coal mine were analyzed based on 454 pyrosequencing and real-time polymerase chain reaction (PCR). A total of 37,191 high quality sequences were obtained and could be classified into 531, 1730 and 448 operational taxonomic units respectively for archaea, bacteria and fungi at 97% sequence similarity. The Shannon diversity index for archaea, bacteria and fungi were respectively 4.71, 6.29 and 3.86, indicating a high diversity in coal mine bioaerosols. Crenarchaeota, Proteobacteria and Ascomycota were the dominant phyla for archaea , bacteria and fungi, respectively. The concentrations of total archaea, bacteria and fungi were 1.44 × 108, 1.02 × 108 and 9.60 × 104 cells / m3, respectively. Methanotrophs observed in bioaerosols suggested possible methane oxidation in the coal mine. to coal miners, such as Acinetobacter schindleri, Aeromonas cavernicola, Alternaria alternata, Aspergillus penicillioides, Cla This was the first investigation of microbial diversity and abundance in coal mine bioaerosols. The investigation of microbial communities would be favorable in promoting the progress of methane control based on microbial technique and concern on coal miners’ health.