Rapid informative methods for assessing the species and quantitative composition of the microflora of the periodontal and oropharyngeal covering tissues are necessary for operative diagnostics, including those of the dentofacial system. The use of classical bacteriological methods, including seeding, incubation, counting and identification of microorganisms takes up to 5 days, resulting in a significant delay in obtaining the necessary information, which makes it difficult to carry out operative treatment measures. Therefore, the search for means and methods of operative microbiological control is urgent. The present work is devoted to substantiation of MSMM (mass spectrometry of microbial markers) technology application as a means of microbiological control of periodontal and other oropharyngeal biotopes.