Bacterial community structure was investigated by analyzing air samples collected almost weekly on the roof of the Faculty of Science, University of Toyama, Toyama Prefecture, Japan. PCR-DGGE (Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis) was used to analyze changes in the structure of the bacterial communities in the atmosphere. The DGGE profiles showed significant differences among sampling days. Overall, 106 bands were excised from the DGGE gels and subsequently sequenced. About 80% of sequences were affiliated with the phylaProteobacteria, Firmicutes, and Bacteroidetes, and the most common genus was Pseudomonas. We also investigated bacterial communities in Asian dust-containing snow layers on Mt. Tateyama. Interestingly, we detected Bacillus isolates with identical 16S rDNA sequences (AB500941) over 2 consecutive years, and these results might reflect the long-distance transportation of microorganisms from dust source regions.