A large number of bacterial species are found in the periodontal pocket. It has been shown that the composition of the subgingival microbiota can differ significantly between individual pockets in one patient, as well as between different subjects. These different types of microfloras can be characterized by indicator bacteria. These indicator bacteria are strongly associated with active periodontal breakdown. Therefore, these microorganisms can be useful in the periodontal treatment of individual patients. It also supports the use of antibiotics in specific forms of periodontal disease. The application of microbiological data in diagnosis and treatment planning in four severe periodontitis patients is illustrated.