In the last decade, high-throughput 16S rRNA sequencing improved the research of the urinary and female genital tract microbiomes, but the relationships between them have not been definitively determined. A review of the literature on the relationship of microbiomes of the urinary and genital tracts in reproductive age women was performed, based on publications in the PubMed, Google Academy, EBSCO, eLlibrary, ResearchGate databases over the past 20 years. The article highlights characteristics of the microbiomes of the urinary tract and vagina, their classification, the features of microbiomes of healthy women and women with urinary tract infections (UTIs). Non-cultural methods allow to identify a number of anaerobic microorganisms, that were not previously detected in the urine by cultural methods, and to evaluate their role in the pathogenesis of UTIs. It was revealed that bacteria of the genus Lactobacillus are representatives of the normal microbiome not only of the vagina, but also of the urine bladder. However, despite the important role of the urinary tract microbiome in the pathogenesis of pregnancy complications, studies on the relationship between the microbiomes of the urine bladder and vagina are contradictory. In most of them, patients of reproductive age are combined with pre- and postmenopausal women, healthy patients with patients, having symptoms of urinary tract infections. Almost half of the studies used voided urine instead of urine, obtained by the catheter, which does not exclude contamination of samples with genital microflora. Further studies are needed to assess the relationship of the urinary and vaginal microbiomes, which will allow further development of methods for their correction.