The development of random amplified polymorphic DNA (RAPD) and expressed sequence tag-derivedsimple sequence repeats (EST-SSRs) provided a useful tool for investigating Korean ginseng genetic diversity. In this study,18 polymorphic markers (7 RAPD and 11 EST-SSR) selected to assess the genetic diversity in 31 ginseng accessions (11Korean ginseng cultivars and 20 breeding lines). In RAPD analysis, a total of 53 unique polymorphic bands were obtainedfrom ginseng accessions and number of amplicons ranged from 4 to 11 with a mean of 7.5 bands. Pair-wise genetic similaritycoefficient (Nei) among all pairs of ginseng accessions varied from 0.01 to 0.32, with a mean of 0.11. On the basis of theresulting data, the 31 ginseng accessions were grouped into six clusters. As a result of EST-SSR analysis, 11 EST-SSR mark-ers detected polymorphisms among the 31 ginseng accessions and revealed 49 alleles with a mean of 4.45 alleles per primer.The polymorphism information content (PIC) value ranged from 0.06 to 0.31, with an average of 0.198. The 31 ginsengaccessions were classified into five groups by cluster analysis based on Nei’s genetic distances. Consequently, the results ofginseng-specific RAPD and EST-SSR markers may prove useful for the evaluation of genetic diversity and discrimination ofKorean ginseng cultivars and breeding lines.