Background : In this study, a total of 46 breeding lines consisting of native ginseng collections from Geumsan was analyzed and clustered for the selection of Geumsan native ginseng in Korea using DNA markers. Methods and Results : We collected 46 Ginseng breeding lines from Geumsan : GS97-25 - GS00-58. Analyses of the genetic characteristics of the collection were conducted for extraction gDNA using sprout. 46 Ginseng breeding lines from Geumsan could be identified polymorphism using the selected 5 primer. We determained that the 46 breeding lines analyzed could be classified into 5 groups with similartiy value of 0.77 in dendrogram derived from the cluster analysis based on STS-markers. Group 4, which is the largest one, contained 19 collertions (41%). Conclusion : These finding could be used for morphological and genetic characteristics for produced native ginseng in Geumsan area. Futhermore, We could be used diverse genetic resources for Ginseng breeding.