Results revealed that for the outdoor environment, larger size (>3.3 μm) bacterial species dominated, while for the indoor environments those of smaller size (<2.1 μm) did. Use of the high power level (700 W) in general resulted in lower culturable bacterial counts regardless of the sampler stage and the sampling environment. The inactivation efficiencies of the microwave treatment were shown to strongly depend on the environments and the microwave energy dose under the experimental conditions tested. PCR-DGGE analysis indicated that use of the high power microwave irradiation (31.5 kJ) generally resulted in less culturable bacterial aerosol richness, while for medium (22 kJ) and low (7.1 kJ) energy doses their culturable species richness appeared to be similar to those of the control experiments. In contrast, smaller (1.1?.2 μm) culturable fungal species were found to dominate regardless of sampling environments. In addition, culturable bacterial aerosol gene mutations with a high frequency after the microwave treatment were detected in the colonies developed. The results from this study provide further information in developing microwave-based bioaerosol inactivation technology.