The purpose of this study was to investigate the distribution of Chlamydia trachomatis (CT) genotypes in infective diseases of the female lower genital tract, especially in cervical diseases. This study included 128 CT-positive women. DNA was extracted from cervical swabs. Omp1 gene PCR-RFLP and sequencing were used to confirm the subtypes of CT. The association of subtypes with age, clinical symptoms, cervical cytology, and biopsy results was further analyzed. Omp1 gene PCR-RFLP and sequencing showed that the order of prevalent CT genotypes in the female lower genital tract was D (n=38, 29.69%), followed by E (n=28, 21.88%), G (n=21, 16.41%), and F (n=16,12.50%). Genotypes J, H, and K were comparatively rare. Genotype I was not identified in our samples. Further analysis showed that patients with genotype G were more frequently co-infected with other bacteria. Genotype G was also associated with mucopurulent cervicitis (MPC) and cervical intraepithelial neoplasia (CIN). Patients with genotype E were commonly co-infected with HR-HPV. Although genotype D was the most prevalent, it was a relatively low-risk type. These results provide information on distribution of CT genotypes in infective diseases of the female lower genital tract, which is instrumental to developing a vaccine for CT.