Health implications of indoor air quality (IAQ) have drawn more attention since the COVID epidemic. There are many different kinds of studies done on how IAQ affects people's well-being. There hasn't been much research that looks at the microbiological composition of the aerosol in subway transit systems. In this work, for the first time, we examined the aerosol bacterial abundance, diversity, and composition in the microbiome of the Seoul subway and train stations using DNA isolated from the PM samples from each station (three subway and two KTX stations). The average PM mass concentration collected on the respective platform was 41.862 µg/m, with the highest average value of 45.95 µg/m and the lowest of 39.25 µg/m. The bacterial microbiomes mainly constituted bacterial species of soil and environmental origin (e.g., Acinetobacter, Brevundimonas, Lysinibacillus, Clostridiodes) with fewer from human sources (Flaviflexus, Staphylococcus). This study highlights the relationship between microbiome diversity and PM mass concentration contributed by outdoor air and commuters in South Korea's subway and train stations. This study gives insights into the microbiome diversity, the source, and the susceptibility of public transports in disease spreading.