Asian-dust events, which include the Asian-desert natural dust and the pollutant anthropogenic dust, disperse airborne microorganisms from Asian continent to Japan island across the Sea of Japan, and significantly impact ice-cloud formation, biological ecosystems, and human health in downwind areas. However, the airborne microbial changes during the cross-border transport process have rarely been investigated in detail. In this study, air samplings were sequentially collected at the top of buildings within the Asian continental site, Yongin, and Japan island site, Yonago, during the dust event season from March to June 2015, for understanding the variations of airborne prokaryotic communities during the cross-border transport processes. At the both sampling sites, aerosol concentrations increased during the natural and anthropogenic dust events, indicating the microbial and mineral dispersions by dust events. The 16S rDNA sequencing database of the air samples revealed that the prokaryotic communities significantly varied between natural dust event days and non-dust days. In the both cities, the relative abundances of Firmicutes (Bacilliceae) positively related with the increase of mineral particle concentrations (dust event occurrences). The Actinobacteria increased during dust event only in Yongin and this positive relation disappeared in Yonago. During the cross-border transport process, spore-forming bacteria Bacilliceae could be selected by the atmospheric stressors. The marine bacteria belonging to Alpha-proteobacteria dominantly increased specific to Yonago, suggesting the accumulation of marine aerosols in island area. The air samples collected during non-dust days predominantly contained regional-origin bacteria which are associated with plant bodies, freshwater environments, and animal fecal matters. Asian-desert natural dusts carry several populations of airborne prokaryotes, which would be modified or removed by anthropogenic pollutants, marine-origin aerosols and atmospheric-stressor selection during the cross-border transport process.