Selenium is an essential trace element for human beings and animals. It primarily exists as inorganic or organic selenium species such as Se2- , Se0, Se4+ and Se6+ in the environment. Microorganisms play an important role in the transformation of selenium speciation, which predominantly drive the geochemical cycle of selenium in the geological environment. In this paper, the focus is placed on the microbes in relation to selenium, the action mechanism of microbes during the transformation of selenium speciation, and the recently developed methods for studying microbes on selenium.