This study was subjected to assess the genetic diversity of Condonopsis javanica (Blume) Hook f. germplasm in Vietnam for the purposes of conservation and its breeding for planting expansion. Samples of 15 natural and cultivated accessions were collected throughout the country with two major areas of distribution in Northwest Highlands (Lao Cai, Ha Giang, Son La) and Western Highlands (Lam Dong, Kon Tum). DNA of 15 accessions were isolated and amplified by 12 arbitrary primers. A total of 106 RAPD-PCR loci were detected, among which 88 loci (83%) were polymorphic, whereas the other 18 (17%) were homogeneous for all the collected accessions. The cluster analysis showed that 15 accessions were divided into 2 obviously distinct groups. One consisted of 5 accessions collected in Northwest highlands, while the other consisted of 10 remaining accessions collected in West highlands. Thus, RAPD-PCR results indicated that there was abundant genetic diversity amongst natural and cultivated population of C. javanica in Vietnam and their genetic relationship appeared to be related to their geographic distance. Thus, germplasms at geographic distance should be subjected to the conservation and breeding programs of this medicinal plant species.