The article focuses on the problem of studying the antibiotic resistance of microorganisms inhabiting the natural environments of the human and animal organism. It analyzes some data published in Russian and world literature on the importance of this problem in the field of public health, veterinary medicine, the existing mechanisms of the emergence of antibiotic resistance in pathogens and forms of acquired resistance. Widespread use of antibiotics in medicine and veterinary led to the emergence of highly resistant pathogens thus creating both an epizootic and epidemiological problem (A.N. Panin et al., 2017). Extensive use of antimicrobials resulted in the selection of resistant strains among the species of commensal, saprophytic and opportunistic microflora. While resisting the effects of antimicrobial agents, bacteria use different sets of defense mechanisms simultaneously and create new counteraction strategies during the evolution (M.A. Shkurat, I.O. Pokudina, D.V. Battalov, 2014). On the one hand, this is due to the evolution of antibiotic resistance genes determining the formation of new molecular mechanisms of resistance, and, on the other hand, to the formation of new mechanisms of adaptation and maintenance in microecosystems. The latter led to the evolution of microbial communities and the emergence of new nosological units. Microbial communities, interacting with each other, create a barrier (biofilm) as a protective factor against antibacterial agents (D. Hughes, D.I. Andersson, 2017). Currently, the microbial communities of the potentially pathogenic microflora, which are stable by species composition, are widely spread, which is manifested by the occurrence of mixed infections. That raises new problems of ensuring the health of animals and humans.