Tadayasu Sawaki has a gift: he can see all kinds of microbes, from the ones that ferment sake to everyday bathroom mold. Not only that, but they're not scientifically accurate but instead cute chibi creatures. When he enters an agricultural university and a professor finds out about his gift, he begins to meet new people that help him discover more about his abilities and himself.

Moyashimon was published in English as Moyasimon: Tales of Agriculture by Del Rey Books, who printed the first two volumes from November 24, 2009 to June 22, 2010, before becoming defunct.