The sites in the genital tract from which mycoplasmas could be recovered at various stages of the estrous cycle were studied in five Standardbred mares naturally infected with Mycoplasma. Mycoplasma equigenitalium and Mycoplasma subdolum were most frequently isolated from the clitoral fossa as compared to the vagina, cervix, and uterus. The lowest isolation prevalence was observed in the uterus. The recovery of Mycoplasma spp. from the clitoral fossa did not differ at any stage of the estrous cycle; however, recovery from the vagina, cervix, and uterus was variable during the cycle and more organisms were recovered on the day of ovulation than at any other time. From these results it was concluded that the clitoral fossa is the most likely "ecological niche" for Mycoplasma spp. in the mare. Ureaplasmas were not isolated.