The aim of this review is to investigate the relationship of oral microbiota with several oral and related diseases, mainly dental caries and periodontitis, and their effects on general health. We shared the results of the studies and the results of the research which are still in the research stage. Specifically, we aimed to introduce and discuss the course of oral microbiota transplantation (OMT) and the process ahead. Microbiota plays an important role in many metabolic events such as modulation of glucose and lipid homeostasis, satiety regula- tion, energy and vitamin production, as well as anti-carcinogenic and anti-inflammatory effects. The most intense colonization area in our body is the oral cavity, followed by the gastrointestinal tract, which contains hundreds of different bacterial, viral and fungal species The diversity in the oral microbiota is shaped by the micro-environmental conditions according to the host’s systemic condition, diet, genetic predisposition and the efficacy of antimicrobial agents in saliva. While the microorganisms in the oral microbiota continue their symbiotic relationship with the host, the variation in the proportion of certain species with the potential for pathogenicity in the ecological flora results in some oral and systemic diseases. In oral medicine, oral microbiota transplantation (OMT) has been hypothetically inspired by fecal microbiota transplantation. Oral microbiota transplantation aims to transfer oral biofilms from a healthy donor to the patient with caries or periodontitis. Ongoing and future studies should provide new information about oral microbiota and how a disbiotic microbiota can be successfully modified with a health-friendly flora.