Although mercury (Hg) is toxic at all valence states, organic Hg, especially monomethylmercury (MeHg, CH₃Hg⁺, methylmercury), is more toxic than inorganic Hg (Hg(II), Hg²⁺). As Hg is predominately methylated via bio-methylation, studies on the mechanism of Hg bio-methylation by microorganisms are particularly important. It is widely accepted that MeHg is mainly produced by anaerobic microorganisms in the environment, and the Hg-methylating process is a cellular reaction. Hence, the production rate of MeHg is not only related to the presence and activities of Hg-methylating anaerobic microorganisms, but also the transport of Hg(II) into microbial cells and the biochemical reactions for forming MeHg in the cells. Therefore, this review described the current state of knowledge on: 1) what kind of microorganisms can methylate Hg; 2) what pathways are the Hg(II) take to enter into the microbial cells; 3) what kind of biochemical reactions happen in the cells; and 4) biogeochemical factors affecting Hg methylation, which are critical to elucidate the regulating mechanisms of Hg methylation by microorganisms. Simultaneously, the existing issues or controversies on biotic Hg methylation were also discussed.