<div><p><i>Epimedium</i> species has gained prime importance due to their medicinal and economic values. Therefore, in this study, 26 genomic SSR and 10 EST-SSR markers were developed for 13 medicinal species of the <i>Epimedium</i> genus and one out-group species <i>Vancouveria hexandra</i> W. J. Hooker to explore the existing genetic diversity. A total of 100 alleles by genomic SSR and 65 by EST-SSR were detected. The genomic SSR markers were presented between 2–7 alleles per locus. The observed heterozygosity (<i>H</i><sub>o</sub>) and expected heterozygosity (<i>H</i><sub>e</sub>) ranged from 0.00 to 4.5 and 0.0254 to 2.8108, respectively. Similarly, for EST-SSR, these values were ranged from 3.00 to 4.00 and 1.9650 to 2.7142. The number of alleles for EST-SSR markers ranged from 3 to 10 with an average of 3.51 per loci. It has been concluded that medicinally important species of the genus <i>Epimedium</i> possesses lower intraspecific genetic variation.</p></div
