The breed was first identified in the historical record in 1697 when the Akizuki family of the Takanabe Clan rounded up feral horses and developed a pool of breeding stock. Today, the Misaki is classified as an endangered but "maintained" breed, with only about 100 living animals. This population has remained relatively stable for the past 20 years, up from a low of 53 individuals recorded in 1973. The Misaki ponies are a popular draw for tourists in the region and were designated a National Natural Treasure following the end of World War II.