Tadayasu Sawaki has just enrolled in an agricultural university in Tokyo with his long-time friend Kei Yuuki. Although not known outside a close circle of friends and family, Tadayasu has the unique ability to see and communicate with microbes, which appear larger and look different to him than they do to a normal person's eyes. This catches the attention of Keizou Itsuki, a professor at the university and an old friend of Tadayasu's grandfather who specializes in microbiology and fermentation. Thus begins Tadayasu's tutelage under Professor Itsuki, aided by his graduate student Haruka Hasegawa, as he attempts to adjust to his new life at the university.

Moyashimon won the 2008 Tezuka Osamu Cultural Prize's Grand Prize and the 2008 Kodansha Manga Award for general manga. It was also nominated for the 1st Manga Taishō award in 2008.