Air purifiers with high-efficiency particulate air (HEPA) filters remove not only particulate matter but also airborne microorganisms in indoor environments. We investigated the bacterial community in HEPA filters (used for 1 year) and that in the floor dust of 12 office rooms in Beijing. We found that the viable bacteria proportion in the filter was significantly higher than that in the floor dust (p < 0.001). The Non-Metric Multi-Dimensional Scaling analysis showed that the bacterial communities in the filters and dust were significantly different (p = 0.001). The Chao1, Shannon-Wiener and phylogenetic diversity values in the filter were significantly higher than those in the dust (p < 0.001). The predominant bacterial classes in the filter were Alphaproteobacteria and Actinobacteria, whereas those in the dust were Bacteroidia, Clostridia and Bacilli. Human occupancy contributed more to the bacterial community in the filter than that in the dust. Klebsiella and Alloprevotella in the dust and filters positively correlated with the occupancy density. Soil bacteria contributed to a significantly higher proportion of the bacteria in the HEPA filter (p < 0.001). In contrast, human oral, indoor air and outdoor haze contributed to a higher proportion of the bacteria in the dust samples (p < 0.001, p < 0.01 and p < 0.05, respectively). As HEPA filters serve as an ecological niche for indoor bacteria, they should be carefully investigated during the assessment of indoor environmental health. People spend the majority of their time indoors, wherein air pollution levels highly correlate with outdoor pollution levels 1-6. In recent years, haze pollution, fine particulate matter (PM) in particular, has been reported to increase human mortality rates owing to the development of heart disease 7,8 , stroke, respiratory disease 9 and lung cancer 10,11. The level of air pollution in China is substantially higher than in many developed countries 12. Moreover, its threat to public health has become a serious concern, particularly concerning haze events 13. Thus, an effective technology is essential for the removal of PM from indoor environments during periods of haze. To this end, air purifiers with high-efficiency particulate air (HEPA) filters are widely used in the indoor environment, particularly in areas with heavy haze 14. People are exposed to various microbes in indoor environments. Many factors could affect indoor microbial composition, including human occupancy, occupant behavior, pets and outdoor environment 15-18. The air purifier was mainly used to remove indoor PM, partly comprising microorganisms. Microbes in the air could be transmitted to the HEPA filter in the air purifier. Suzuki et al. (2003) collected swab samples from the air purifier filters in the houses of seven healthy children with varicella. They found the varicella-zoster virus was detected in 29% of filters in air purifiers by day 3 19. Furthermore, Maus et al. (2001) studied the effect of the filters on the viability of microbes. They reported microb...