To determine the prevalence of genital mycoplasmas and ureaplasmas in the pharynges of Japanese female sex workers practicing fellatio on their clients, vaginal swabs and throat washings were collected from 403 female sex workers attending a clinic in Kyoto, Japan, for regular screening of gonococcal and chlamydial infections. Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum in vaginal and throat specimens were tested by nucleic acid amplification tests. The prevalence of N. gonorrhoeae, C. trachomatis, M. genitalium, M. hominis, U. parvum, and U. urealyticum in the genitals was 1.7%, 7.2%, 1.7%, 19.6%, 40.4%, and 10.2%, respectively, whereas their prevalence in the pharynges was 4.0%, 2.0%, 0%, 1.2%, 0.2%, and 0.7%, respectively. Gonococcal infection in the pharynx was significantly associated with gonococcal infection in the genitals. Chlamydial infection in the pharynx was also significantly associated with chlamydial infection in the genitals. M. hominis, U. parvum, and U. urealyticum were all detected in vaginal swabs and in throat washings; however, M. genitalium was detected in vaginal swabs but not in throat washings. For each of these genital mycoplasmas and ureaplasmas, a positive test result in the pharynx was not significantly associated with a positive result in the genitals. M. hominis, U. parvum, and U. urealyticum were detected in throat washings, but M. genitalium was not. These findings do not necessarily rule out the transmission of M. genitalium from the pharynx to the urethra by orogenital sex.