Japanese people have developed various fermented food products all over the country since ancient times. In recent years, these fermented food items have been attracting attention both at home and abroad because they are believed to help us live a healthy life. However, when we conduct research on Japanese fermented foods, we need to take into account the diversity of ways in which they are made, preserved, and seasoned, in addition to how their ingredients are mixed and matched as well as the meaning of eating them. Where does this diversity come from? In answer to that question, we focus on natto, fermented soybeans, as one of the main fermented foods in Japan, and discuss the regional characteristics of natto food culture and propose a new method to study the diversity of food culture.