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Objective: This study was aim to investigate the relationship of vaginal bacterial species with High-Risk Human Papillomavirus (HR-HPV) and bacterial vaginosis (BV).Methods: One hundred and twenty-one women were included in the study. Gram stain was performed for the diagnosis of BV and evaluated according to the Nugent score. HR-HPV diagnosis was made by real-time PCR . Detection of vaginal microbial species and Gardnerella vaginalis subtypes were also performed by real-time PCR.Results: The prevalence of BV was found as 38.8%. The mean number of species was found significantly higher in BV-positive samples compared to BV-intermediate and BV-negative samples (p=0.001). Lactobacillus iners (p=0.036), BVAB2 (p=0.043), Provetella spp. (p=0.015), Leptotrichia/Sneathia (p=0.001), Megaspheara (p=0.048) were found to be associated with bacterial vaginosis. Gardnerella vaginalis subtypes were evaluated in 50 randomly selected samples. The most common strain that was found was “clade 4”. The prevalence of HR-HPV was 9.9%. HPV 16 was the most common HR-HPV type (58.3%). There was no significant difference between the mean value of Lactobacillus sp. HR-HPV-positive and negative samples (p=0.23). No association was found between the specified species and HR-HPV-positive samples (p=0.436).Conclusion: Bacterial diversity was greater in BV-positive patients and BV was significantly associated with Lactobacillus iners, Megaspheara, BVAB2, Provetella spp. and Leptotrichia / Sneathia.