Abstract: Objective To understand the indoor airborne microorganism condition in the underground stations of Shanghai subway system. Methods The air samples from subway station platform were collected according to national guideline and the bacteria and fungi were detected, while the outdoor air samples outside station were collected as compared samples. Results The number of bacterial colonies of samples collected at platforms was lower than that collected outdoor(P<0.05),while the number of fungal cultures showed the opposite result. The most microorganism were mainly adhere to the particles with size of 0.65 μm-4.70 μm. Conclusion The particle size of microbial aerosol under 5.00 microns in subway stations should be monitored, since it has a harmful effect on human health.