This study aims to consider the microbial distribution in oral disease, as well as gene analysis and expression, in elucidating: 1, the fundamental underpinnings of oral disease, and 2, the potential relationship between oral diseases and systemic health. A key focus is identifying the microbiota associated with oral disease manifestations characterized by both conventional microbiological and molecular methods. Variations in the observed microbial populations characterized by conventional and molecular approaches have been identified for caries, periodontitis, peri-implantitis, and stomatitis. The discovery of therapeutic approaches for oral disease will require comprehensive microbial and genomic analysis. This study evaluated the current state of the relevant microbial and genomic information for several prevalent oral diseases.