There are tens of billions of microorganisms on the surface of the human body and in the body, which together with humans form a “superorganism”. These microorganisms are not just bystanders, they have evolved with us to participate in the normal life activities of the human body and to maintain the balance of the internal environment. Imbalances in the digestive microbiota are associated with susceptibility to many diseases, including obesity, malignancies, liver disease and digestive tract disorders. It is well established that there is a direct or indirect link between the microbiota and the host immune response, and the mechanism of their interaction is one of the hot topics of research today. There is increasing evidence that microbiota alterations are associated with certain autoimmune diseases, such as type I diabetes, celiac disease, and rheumatoid arthritis. In rheumatoid arthritis both in animal models of the disease and in patients, there are alterations in the composition and diversity of the flora. Artificial interventions in the flora composition of animal models of disease can alter the severity of the disease. Among rheumatoid arthritis, periodontitis was first thought to be associated with the disease, and tooth extraction for rheumatoid arthritis treatment was even popular in the early 20th century. Current studies have found that even in populations with the same hygiene status, patients with rheumatoid arthritis still have a higher incidence of periodontitis. Among other things, infection with Porphyromonas gingivalis induces the production of anti-cyclic citrulline autoantibodies in rheumatoid arthritis and may therefore be a cause of rheumatoid arthritis. In addition respiratory bacteria and intestinal bacteria have been found to have pathological mechanisms associated with rheumatoid arthritis. However, the question of whether microbiota dysbiosis causes rheumatoid arthritis or rheumatoid arthritis causes microbial dysbiosis remains unresolved. The investigation of the role of microorganisms in rheumatoid arthritis may provide new entry points for insight into the onset and progression of the disease and the development of new treatments.