It is one of eight horse breeds native to Japan.

Numbers subsequently recovered slightly;[2]: 94  85 head were recorded in 2008.

[1] The conservation status of the breed was listed as "critical" by the FAO in 2007.

[3]: 71 In 2003, genetic analysis using microsatellite data found the Yonaguni to be most closely related to the Miyako and Tokara small-island breeds, and less closely related to various Mongolian horse breeds than were the Dosanko and Kiso breeds of the main islands of Japan.

[4]: 378 Like the other Japanese island breeds, the Yonaguni is small.