Abstract: Background and Objective: Dysosma tonkinense (Gagnep.) M. Hiroe (Berberidaceae) is a precious medicinal plant that distributes in Vietnam and Southern areas of China. The dried roots and rhizomes of D. tonkinense have been used in folk medicine for the treatment of poisonous snake bite, ulcer and cancer. This study aimed to analyze the genetic diversity of 20 accessions of D. tonkinense collected from 13 geographical regions of Vietnam through ISSR and RAPD markers. Materials and Methods: The 24 ISSR and 11 RAPD primers were examined in this study. Twenty four ISSR primers produced 136 PCR bands, of which 117 were polymorphic with an average of 5.67 polymorphic loci per primer and only 19 loci were monomorphic. Results: RAPD marker detected 79 loci, 52 of these markers were polymorphic with an average of 7.18 loci per primer. The similarity coefficient ranged from 0.59-0.85, 0.60-0.98 and 0.62-0.89 for ISSR, RAPD and pooled ISSR-RAPD data, respectively. The UPGMA dendrogram generated using ISSR-RAPD data showed that, at the genetic similarity of 72%, 20 accessions were separated into 3 distinct clusters. Conclusion: The present finding indicates that the marker tools ISSR and RAPD combined can be used in determining the genetic relationship between the accessions. It may be concluded that the genetic diversity among the 20 D. tonkinense accessions collected in several locations in Vietnam could be utilized for the conservation and breeding programs especially for some endangered species such as D. tonkinense.