Kuzu-mochi, which is a traditional Japanese sweet, is made from fermented wheat starch. In this study, we examined changes in wheat starch granules and the microflora during the fermentation of wheat starch. Large, broken granules of starch and gram-positive bacilli were observed during the fermentation process. The pH ranged from 3 to 4 throughout the process. Lactic acid and acetic acid were detected in each fermentation period, with lactic acid being the predominant acid. This result indicates that lactic acid bacteria (LAB) are heterolactic fermenters. Viable cell count was determined at the same pH as that of the fermentation medium, and microorganisms that can grow in acidic conditions were isolated. The microflora present during the fermentation process included 2—3 species of aerobic bacteria, fungi and yeast, and approximately 10 species of LAB. PCR-denaturing-gradient-gel-electrophoresis profiles indicated that the microflora remained stable from the pre-fermentation period to about 6 months post-fermentation. Furthermore, the supernatant collected during the pre-fermentation period showed starch hydrolysis activity, and wheat starch was broken by its enzyme. These results suggest that the bacterial community present at the pre-fermentation period can serve as a starter culture for the traditional processing of fermented wheat starch.