The identification of polyvirulent strains of Lactobacillus spp. bacteria with associative interaction with protozoa Blastocystis hominis in vivo was carried out. Lactobacillus spp. and B. hominis strains were obtained from the feces of 396 patients undergoing examination for intestinal dysbiosis. Identification was carried out using microscopic, bacteriological and parasitological methods. 112 reference strains of lactobacilli NK1 and K3SH24 deposited at the Institute of Genetics and Breeding of Industrial Microorganisms were used as control. The degree of virulence of the simplest blastocysts was determined by intraperitoneal administration to white mice (weighing 17.4+1.5 g) 0.5 ml of a culture suspension of the studied microorganisms grown on Suresh medium. Primers to several genes determining the ability to form type 1 fimbriae, type S and P fimbriae, bacterial adhesin intimin and hemolysin were used in the investigation. Testing of 396 Lactobacillus spp. strains isolated from microsymbiocenoses with Blastocystis hominis of varying degrees of virulence showed that the dynamics of detection of pathogenicity genes in lactobacilli increased with an increase in the degree of virulence of protozoa. Most often, in the general pool of lactobacillus strains, the desired amplicons were detected using primers to the fimA gene (up to 67.9%). During associative interaction with moderately and highly virulent blastocysts, an increase in the heterogeneity of the lactobacillus population was revealed, manifested by an increase in the frequency of detection of all studied genetic determinants of pathogenicity, compared with Lactobacillus spp. strains isolated from associations with avirulent B. hominis and in the control group.