There are two types of starter cultures used in Japanese rice wine (sake) fermentation, namely, sokujo-moto and yamahai-moto. Analyses of microbiota changes during sake production using yamahai-moto have already been reported. In this study, we analyzed microbiota changes during sake production using sokujo-moto. In addition, we sequenced bacterial DNA from the water used in sake production. The Lactobacillus DNA sequences, which are frequently detected during sake production using yamahai-moto, were not detected during sake production using sokujo-moto, indicating that the Lactobacillus DNA detected in sakes made from yamahai-moto is from the fermentation starter. Most bacterial DNA sequences detected in water were not found in the production samples of sake suggesting that these bacteria do not proliferate during sake production. Thus, most of the bacterial DNA sequences detected during the production may be from the bacterial contamination during the production process.