ResultsAmong 375 Chlamydia trachomatis positive cervical swabs, the prevalence of coinfection with Neisseria gonorrhoeae, Candida albicans, Trichomonas vaginitis, Vulvovaginal candidiasis, and HPV were 0.8%, 2.7%, 2.4%, 10.1% and 15.5%, respectively. 306 were genotyped successfully, and nine genotypes were identified. The most common genovar was E (25.16%, 77/306), followed by J (22.55%, 69/306), F (17%, 52/306), D (14.4%, 44/306), K (7.2%, 22/306), G (6.9%, 21/306), H (5.2%, 16/306), B (1.0%, 3/306), Ia (0.7%, 2/306). Genotype H was associated with abnormal cervical cytology [p = 0.006, aOR = 8.16 (1.86–36.6)]. However, this study observed no association between Chlamydia trachomatis genotypes and any genital clinical symptoms.