Airborne microorganisms are transported from ground surfaces up to the free troposphere and are fall down to downwind areas, causing the impacts on biological ecosystems, human life, and cloud formation. However, the vertical transport of airborne microbial communities below the free troposphere has rarely been investigated because sampling techniques should be sophisticated for the direct collection of microbial cells at several altitudes. In this study, air sampling was performed using an aircraft at 3000 m over the Noto Peninsula in Japan, where free tropospheric winds carry aerosols from continental areas. The samples at 800m and 10m were also collected using a balloon and on the building, respectively, in Suzu city (37.5?N, 137.4?E) located at north edge of the Noto Peninsula. During the sampling period at March 10, 2013, the tropospheric air mass came from Gobi desert area by westerly wind. The air samples collected at 3000m included aerosol particles significantly suggesting that winds carry aerosol particles from continental areas. Pyrosequence analysis targeting 16S rRNA genes (16S rDNA) revealed that bacterial community at 3,000 m was mainly composed of terrestrial bacteria belonging to Bacilli and Actinobacteria, while that at 1,000 m and 10 m altitudes consisted primarily of marine bacteria such as Cyanobacteria and Alpha-proteobacterium members. Moreover, 16S rDNA clone analysis supported that some dominant phylotypes were identical to marine and terrestrial bacterial species. In particular, Bacillus members were identical to the isolates obtained from Kosa dust source region suggesting that they were possibly transported from continental areas. In summary, tropospheric air mass from continental and marine bacterial communities would contribute to the vertical dynamics of airborne bacterial communities in atmospheric column over downwind area.