Many sexually transmitted diseases are caused by bacteria. While we fairly well understand the role of some microorganisms in the development of genitourinary tract infections, there is still a vast majority of those whose contribution is unclear. It is believed that sexual partners share their genitourinary microbiota, meaning that treatment regimens should be the same for both of them. This article reports results of the study of seminal and cervical microbial communities conducted in 50 married couples who did not use barrier birth control and did not take any antibiotics at least 3 months before the study. All couples presented with complaints of primary or secondary infertility, recurrent miscarriages or sought preconceptional counseling. The mean age of male and female participants was 34.8 ± 7.8 and 30.4 ± 6.2 years, respectively. Samples of the seminal fluid and vaginal secretions were studied by real-time polymerase chain reaction (real-time PCR) with Androflor and Femoflor reagent kits. The following bacteria were more frequent in the vaginal microbiota than in the seminal fluid: Lactobacillus spp. (p < 0.005), Eubacterium spp. (p = 0.002), Gardnerella vaginalis (p = 0.002), Megasphaera spp./Velionella spp./Dialister spp. (p = 0.004). Ureaplasma spp. was 3 times more frequent in women, Mycoplasma hominis was 4 times more frequent in men; however, this difference was not significant.  In 4 (8 %) couples both partners had normal microbiota; 23 (46 %) couples shared at least one microbiota resident. Also, microbial communities were totally different in 23 couples. The obtained data indicate that both sexual partners should be examined to decide on the most effective treatment for each of them. Qualitative and quantitative real-time PCR assays Androflor and Femoflor provide comprehensive data essential for adequate treatment planning.