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Dysosma versipellis (Berberidaceae) is an important threatened medicinal plant (TMP) species. Here we isolated nine polymorphic microsatellite loci from D. versipellis using a modified biotin-capture method. Our isolated loci provided SSR markers with polymorphism of 2–7 alleles per locus. The expected and observed heterozygosities ranged from 0.507 to 0.864 and from 0.360 to 0.720, respectively. These markers would be the useful tools for analyzing questions concerning population genetic structure and mating system of D. versipellis.