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Nineteen genomic SSR markers were developed using inter-simple sequence repeat (ISSR)- suppression PCR technique in Bupleurum chinense DC., a widely used Chinese medicinal plant. A total of 126 alleles were detected across 22 individual plants of B. chinense DC. f. octoradiatum (Bunge) Shan et Sheh, with an average of 3 - 13 alleles per locus. The observed heterozygosity (HO) and the expected heterozygosity (HE) values ranged from 0.23 to 1.00 and from 0.29 to 0.92, respectively. Nine loci deviated from Hardy-Weinberg equilibrium (HWE) (P < 0.05) and eight pairs of loci showed significant linkage disequilibrium (LD) (Fisher’s exact test, P < 0.01). The species transferability of these genomic SSR markers was also detected in seven other Bupleurum species. Eight SSR markers were successfully amplified in all tested species. In addition, forty four EST-SSRs which can be amplified with expected sizes were identified from a B. chinense root cDNA library. The genomic SSR markers and potential EST-SSR markers developed in the present study should be useful for genetic diversity and molecular marker assistant selection breeding research in Bupleurum species.