Kōji, employed for centuries in the Japanese brewing industries to mass manufacture sake, soy sauce, and miso, is today the “national fungus” (kokkin) of Japan. In a period of crisis beginning in 1960, however, the understanding of the kōji mold as a traditional, edible helper to human lives changed. “Aflatoxin,” produced by a closely related fungus, appeared on the global stage as one of the most potent carcinogens naturally found in food. The kōji mold came to be perceived in a new, ambivalent light—as a potential carcinogen and source of environmental contamination in the body. In response, mycologists’ efforts, especially in Japan, to reclassify kōji as a distinct object separate from the aflatoxin-producing mold resulted in a tentative narrative of kōji evolution, in which human cultivation had created a domesticated, safe, edible microbe that was different than its wild, carcinogenic, inedible close relative. When examined carefully, this evolutionary narrative of human control is simultaneously a reflection of the intractability of microbes—of eating, domesticating, and ultimately knowing them.