In order to promote conservation of the traditional Tokara horse in its remaining three breeding areas in Japan (Nakanoshima, Kaimondake, and Iriki), we genotyped 123 horses using 31 microsatellite markers and determined their genetic diversity. On average, the number of alleles (N_A), observed heterozygosity (H_O), expected heterozygosity (H_E), and inbreeding coefficient (F_IS) among all horses were 3.0, 0.424, 0.481, and 0.108, respectively. Compared with other endangered horse breeds, we found that, even though the size of the Tokara horse population has recently increased, the N_A, H_O, and H_E of Tokara horses are still notably lower than those of other breeds. Neighbor-joining tree and STRUCTURE analysis showed that the current population of Tokara horses is divided into three subpopulations, corresponding to their respective feeding and breeding areas: Nakanoshima, Kaimondake, and Iriki. This subdivision was also reflected in the N_A of microsatellite DNAs, with four, three, and four different loci showing single alleles in Nakanoshima, Kaimondake, and Iriki horses, respectively. These alleles are considered to have become fixed as a consequence of breeding within the limited number of horses in each area. Since Tokara horses are currently strongly divided into subpopulations, it is vitally important to exchange several horses among their different breeding units in order to maintain the genetic diversity of the Tokara horse as a unique breed. The data obtained in this study contribute toward explaining the history of Tokara horses and also provide important information for future monitoring of population diversity and guiding conservation measures for this endangered breed.