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In recent years, the etiology of periodontitis has tended to be based on the theory of flora imbalance. That is, periodontitis is not caused by specific bacteria but by the breakdown of the oral flora balance, which leads to an immune imbalance. Imbalanced bacterial flora cooperate with each other to produce virulent factors that destroy organism tissues and induce immune cells to produce abnormal levels of cytokines, causing greater damage. This article reviews the initiation of a flora imbalance, the interaction between bacteria, the immune damage of the host and the prevention and treatment of the flora imbalance. The literature review shows that peroxidase released by inflammatory reactions, host immune responses to pathogenic microorganisms and some systemic factors, such as diabetes, can trigger flora imbalance. As a result, ion transport, substance synthesis and metabolism of bacteria change; virulence factors increase; and the oral flora balance is disrupted. Red complex bacteria enter gingival epithelial cells, produce adhesin, and selectively inhibit the expression of specific chemokines, which is beneficial for other pathogenic bacteria to enter gingival epithelial cells. Toxicity factors increase throughout the body, directly destroying body tissues and inducing innate and adaptive immune responses, thus causing related immune damage. The dysbacteriosis model of periodontitis provides a new idea for the prevention and treatment of periodontitis, such as using biological factors, bacteriophages, probiotics and other methods to reduce the number of periodontal pathogens to restore the steady state of periodontal flora.