Human body is inhabited by large number of microbial organisms that form complex ecosystems. Oral cavity is one of the major sites for microbial colonization. Oral microbial diversity is huge as the compositions vary among different oral cavities, different locations within the same oral cavity, or same location at different time points. The differences in compositions and varieties determine the balance of human oral microbial ecosystem, which is directly associated with oral disease or health. This review focuses on the history and new progress of the studies on human oral microbial communities.