Moyasimon follows the life of Tadayasu Sawaki, a first-year college student at an agricultural university, who has the unique ability to see and communicate with micro-organisms and bacteria. Additionally, these organisms look much different to him, and much larger, than what can be seen under a microscope by normal people. This ability has brought him a bit of fame as when he entered the university, Tadayasu discovered that one of the professors there, Keizo Itsuki, already knew about his gift via Tadayasu's grandfather. Professor Itsuki's coworker Haruka Hasegawa has trouble believing what Tadayasu claims at first, but later comes to accept it. Tadayasu enters the university with his good friend Kei Yuki whose family runs a sake brewery.