Together with the worldwide Washoku (traditional Japanese foods and drinks) boom, interest in sake, a traditional Japanese alcoholic drink, is increasing around the world. There are few scientific analyses and studies on the production of sake or the final product itself. We show the diversity of bacterial contaminants during sake production and investigated the effects of different ingredients on sake (for example, amino acids). The koji mold Aspergillus oryzae converts rice starch into sugars, and then, the sake yeast Saccharomyces cerevisiae converts the sugars to ethanol. Comparative studies of the bacterial flora of different sakes have shown that various bacterial species are detected, but that there are few frequently detected bacteria. In addition, the bacterial flora does not vary much during the process of sake brewing, after the koji (steamed rice covered with koji mold) and moto (fermentation starter) are mixed, suggesting that most bacteria contaminate the sake during the process of koji and moto production. Thus, there is the possibility that the contaminating bacteria may grow due to a relationship with the koji mold and/or the sake yeast. The flavor, taste, and quality of sakes differ, even between the same brands of sakes, which may be attributed to variations in the contaminating bacteria during sake production.