Bacterial vaginosis is one of the most common reproductive health problems in women. Lactobacillus spp. play a leading role in the vaginal biocenosis and provide local antimicrobial defense, but not all species are equally capable of protecting the vaginal ecosystem from pathogens. Diagnostic methods in practical healthcare do not allow identification of Lactobacillus spp. species, which limits the ability to comprehensively assess the status of the vaginal biocenosis. We conducted a study in which we compared microscopy data of the examined smear with the detection of Lactobacillus spp. and other microorganisms. The aim of the study was to evaluate the species composition of Lactobacillus spp. from the vagina depending on morphologic characteristics and composition of associated flora. The study included 64 conditionally healthy women of reproductive age from 18 to 35 years old. The study of species composition of the vaginal biocenosis and typing of lactobacilli was carried out by real-time PCR methods. The obtained results were processed using generally accepted methods of descriptive and ordinal statistics. During the study, it was found that the vaginal biocenosis was dominated by species of Lactobacillus spp. L. crispatus, L. vaginalis, L. iners and L. jensenii. L. johnsonii was rarely found, and L. acidophilus was not detected. Typing results showed that the vagina was more frequently colonized by more than one species of Lactobacillus spp. while a single species of Lactobacillus spp. was detected less frequently. A correlation was found between Lactobacillus spp. species and bacilli thickness. If thick bacilli are detected in gynecological smear microscopy, they belong to the species L. crispatus, which has high colonization resistance and is a factor in the stability of the vaginal biocenosis. If smear microscopy reveals thin bacilli, then these are species of L. iners and L. jensenii. These representatives of Lactobacillus spp. are not directly related to the dysbiotic state of the vagina, but may indicate the possible development of dysbiosis in the future.