The breed is small, standing about 11 hands (115 cm). Two small herds of about 108 horses remain on the island ranging free and are rounded up once a year for inspection, removal of pests and inoculation. The Yonaguni are usually chestnut. The head is large with well-placed eyes and relatively small ears; the neck is short and thick; the shoulders tend to be straight; the back is long; the croup is often quite level with a high tail-set; the quarters are slight; the legs often tend to be splayed; the hooves are vertically long and very hard.
The Yonaguni is a small native pony of the southwest islands of Japan. In 1996 there were about seventy-five living Yonaguni ponies on East and North Ranches on Yonaguni Island, located on the west side of the Yaeyama Islands.
Little is known about the origin of the Yonaguni. Horses in Japan can generally be divided into two groups, larger specimens from Hokkaido and smaller individuals from Yonaguni. Many people believe that the small horses were introduced from the southern islands during the Jyomon Period, about two thousand years ago. Professor Ken Nozawa of Kyoto University claimed in 1983 that the gene characteristcs of the breed indicated relationship to the Cheju breed in Korea.