This paper traces the relationship between the upgrading of the sake and soy sauce industries in Japan – specifically the introduction of pure culture techniques and especially for koji (the rice mold used in traditional brewing) – and the activities of agricultural chemists in building culture collections and microbial classification in the early twentieth century. The importance of sake brewing to the country’s tax revenue and economy meant that agricultural chemistry had no real equivalent in Europe or the United States, but grew into the largest discipline in the Japanese life sciences. Within this context scientists, especially at Tokyo Imperial University’s Department of Agricultural Chemistry and the national Brewing Experimentation Station run by the Ministry of Finance, collected strains from tanekoji makers across the country who produced koji starter for the traditional brewing industry, since koji (Aspergillus oryzae, the rice mold necessary for making sake, soy sauce and miso) had been domesticated in breweries for centuries and did not exist in the wild. Their studies attempted to understand which microbe types were ‘useful’ and ‘harmful’ for the brewing process, as well as to classify them in accordance with international systems of taxonomy. At the same time, tanekoji makers had held long-established practices of culturing, selecting and preserving ‘good’ mold types as purely as possible. As these practices were upgraded by research on microbes and Pasteurian practices of pure culture, the ability to produce and sell pure-cultured microbial strains under scientific brand names altered the tanekoji industry. By tracing these transformations in the decades after 1900, the paper examines how natural historical studies of microbes in Japan both incorporated knowledge from and affected the traditional brewing industries.