Panax stipuleanatus Tsai is a type of medicinal plant within north-west Vietnam. In this study, inter simple sequence repeat markers were employed to investigate the genetic diversity of naturally distributed populations classified by habitat for this species. Genetic diversity at the species level was moderate (H eT D 0.254; PPB T D 96.02%). Genetic diversity was not equal in two populations. The result showed higher population genetic diversity in the Lao Cai region (H eBX D 0.266; PPB BX D 91.48%) as compared to those located in Lai Chau region (H eHT D 0.235; PPB HT D 84.66%). The interpopulation gene differentiation was small (G STP D 0.03) with the genetic distance among populations was D P D 0.0103. Gene flow within populations was as high as Nm D 7.36.