The current study examined the antimicrobial resistance of Chlamydia Trachomatis (CT) genital infection during pregnancy in Japan. We requested 2,146 obstetrical facilities that are members of Japan Association of Obstetricians and Gynecologists to provide information of CT screening tests and antimicrobial resistance in pregnant women between April 2020 and March 2021. The prevalence of CT genital infection in Japan was 2.1%. The antimicrobial resistance was recognized in 2.0 and 2.4% of the cases using azithromycin and clarithromycin, respectively. There were no significant differences in the antimicrobial resistance rate between the 2 analogues (P = 0.28). In Japan, azithromycin and clarithromycin have effectively treated genital CT infections during pregnancy.