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Microbiota transplantation has emerged as a novel therapeutic strategy aimed at restoring microbial balance in dysbiotic environments. While fecal microbiota transplantation (FMT) has demonstrated clinical success in gastrointestinal disorders, its conceptual extension to the oral cavity—termed oral microbiota transplantation (OMT)—is gaining increasing attention. Oral diseases such as dental caries, periodontitis, and halitosis are closely associated with microbial dysbiosis, and similar imbalances are implicated in systemic diseases with oral manifestations, including diabetes mellitus, cardiovascular diseases, gastrointestinal disorders, rheumatoid arthritis, and cancer. This review explores the biological basis, mechanisms, clinical applications, and challenges of microbiota transplantation in oral and systemic conditions, highlighting current evidence and future directions.