The present paper introduces the recent progresses on the production mechanisms and environmental fates of microcystins—the most common toxins produced in bloom-forming cyanobacteria, in particular, Microcystis. The review contains three parts:(1)biological origin, structure and properties of microcystins; (2)synthesis, cellular distribution, production and possible function of the toxins; and (3)environmental fates of the toxins. Recent progresses, problems and perspectives in the study of environmental fatesof toxins are viewed and discussed.