Oral microbiota, one of the most diverse human microbiotas, has proved to be important for the maintenance of health and development of diseases. In this reprint, the oral microbiota and key oral microbes in different diseases, such as Alzheimer’s disease, respiratory diseases, oral cancer, cleft palate, and caries, were investigated and summarized. This highlights the importance of why we need to pay more attention to the insights in oral microbiota. Detection techniques, novel biomaterials, small molecules, and probiotics were also developed and discussed in this reprint in order to provide potential regulation and treatment strategies for different diseases related to oral microbiota.