Bacteria of the genus Lactobacillus are inhabitants of the surfaces of human mucous membranes, such as the oral cavity, digestive and urogenital tracts. Moreover, there is evidence that they are found in breast milk and sputum. In view of the many genetic differences, metabolic abilities and other functions of the species included in this genus, a revision of the classification of the genus Lactobacillus is proposed in 2020. Recently, in the scientific medical literature, the issues related to the influence of lactobacilli on the human microbiome, maintaining health and preventing pathological conditions of the body have been actively discussed. This review is devoted to the functional characteristics and analysis of the species diversity of Lactobacillus spp. circulating in various body systems, their participation in the formation and regulation of defense mechanisms. However, negative impacts are also noted, most often associated with the transfer of genetic determinants of resistance to antimicrobial drugs from lactobacilli to gram-negative microbiota.