The processing of archetypal Japanese sushi involves microbial fermentation. The traditional sushi kaburazushi, introduced in the middle ages, is made by fermenting salted yellow tail, salted turnip, and malted rice, and is distinguished from the ancient sushi narezushi, made from fish and boiled rice. In this study, we examined changes in the microbial population during kaburazushi fermentation by pyrosequencing the 16S ribosomal RNA genes (rDNA) of the organisms in the fermentation medium. Ribosomal Database Project Classifier analysis identified 31 genera, among which Lactobacillus drastically increased during fermentation (150-fold increment over 8 d), while the relative populations of the other gram-positive bacteria (Staphylococcus and Bacillus) decreased. Basic Local Alignment Search Tool analysis revealed the dominant species to be L. sakei. This organism constituted approximately 90% of Lactobacillus and 79% of total microbiota. The taxonomic diversity and species richness (assayed by Shannon-Weiner Index and Chao 1, respectively) were not significantly different between middle-ages kaburazushi and ancient narezushi. Both types were characterized by the preferential growth of Lactobacillales.