Introduction. Lactobacillus is main taxa of healthy vaginal microbiome. A decrease in the number of lactobacilli indicates a violation of the equilibrium state of the vaginal microbiocenosis and can lead to colonization of the vagina by potentially pathogenic bacteria and fungi, which is accompanied by the development of infections and various pelvic dysfunctions. Bacteriophages can significantly affect the vaginal microbiome composition. Here we described the study results of potentially active moderate bacteriophages genetic diversity in the genomes of the main vaginal species of lactobacilli based on genomic and metagenomic data. Methods. To assess the possible presence of prophage sequences in the genomes of lactobacilli, 129 genomic assemblies of lactobacilli species L. crispatus, L. jensenii, L. iners and L. gasseri, as well as 4 available viral WGS metagenomes of the vagina from a patient with bacterial vaginosis were analyzed. Results. As a result, a list of 51 sequences of alleged prophages was obtained. The distribution of putative prophages by lactobacillus species had the following structure: 12 were found in 9 of 18 analyzed genomes of L. jensenii, 23 in 17 of 34 analyzed genomes of L. gasseri, 9 in 8 of 56 analyzed genomes of L. crispatus, and 7 in 7 of 21 analyzed genomes of L. iners. Some of the identified prophages resembled the previously described prophages of L. jensenii and L. gasseri, while the others had no analogues. Conclusion. Phages of L. iners described here for the firs time. The identified prophage sequences were specific for each species, and did not occur in other species of lactobacilli. The data obtained can be used to study the role of prophages in the etiology of bacterial vaginosis.