Moyashimon follows the life of Tadayasu Sawaki, a first-year college student at an agricultural univeristy, 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 see 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 father. 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. The Department of Agriculture building on the school's campus is a near identical replica of the real life University of Coimbra in Portugal. The flag at the top of the clock tower also has the same color scheme as the Portuguese flag.