The oral microbiota plays a primary role in the initiation and progression of the periodontal disease. Because of the multiplicity of factors that control the establishment and long-term evolution of the oral microbiota, a great deal of heterogeneity exists in the composition of the periodontal microbiota among individual subjects. Despite these individual differences and the complex interactions between bacteria and the host and among bacteria, an association has been demonstrated between certain species and various forms of periodontal disease. A variety of microbiological diagnostic tests are available to use for evaluation of patients with periodontal disease. A key step in diagnosis of a disease is to identify the causative microorganism. Advanced diagnostic aids are increasingly playing a more vital role in this process, both in identification and treatment of periodontal disease.