A 6-year-old miniature pony mare was examined because of the abnormal appearance of the perineal region. A physical examination revealed an enlarged and penis-like clitoris in the vulva. The owner reported that the horse had frequently exhibited aggressive behavior. Blood and hair root samples were collected for the karyotyping and genetic marker tests. Cytogenetic and molecular analysis showed that the pony had a 64,XY SRY-positive disorder of sexual development (DSD). The owner opted for no surgical removal of the internal genitalia. This report describes the karyotyping and genetic marker analysis of 64,XY SRY-positive DSD in a miniature pony in South Korea.