Epimedium koreanum Nakai， a medicinal plant of critical importance in Northeast China， has experienced severe depletion of its wild populations due to overharvesting. Investigating the genetic diversity of its germplasm and elucidating phylogeographic relationships among populations are therefore essential for developing effective conservation strategies. The research employed ISSR （Inter simple sequence repeat） marker technology. Through preliminary optimization of the reaction system， seven highly polymorphic primers were selected for genetic diversity analysis of 128 samples collected from 14 natural populations in Northeast China. Results showed that these seven ISSR primers amplified a total of 80 bands，with 74 （92.60%） being polymorphic. Number of observed alleles （Na） is 1.6438， effective number of alleles （Ne） is 1.3747， Nei′s gene diversity index （H） is 0.2189， and Shannon′s information index （I） is 0.3290. The WNS population （Wunu Mountain Scenic Area， Huanren county， Liaoning province） showed the highest genetic diversity， while the DLZC population （Dalizi village， Linjiang city， Jilin province） exhibited the lowest. After comparison with other species in the same genus， it was found that the genetic diversity of Epimedium koreanum germplasm resources is at a moderate level. Genetic similarity coefficients among populations ranged from 0.7441 to 0.9700， with genetic distances between 0.0304 and 0.2955. Mantel test showed no significant correlation between genetic and geographical distances， suggesting that population differentiation may be influenced by habitat isolation or reproductive characteristics rather than geographical distance. Genetic structure analysis （Gst=0.2784） indicated that 72.16% of genetic variation occurred within populations. Furthermore， cluster analysis divided the 14 populations into five distinct groups. This study provides fundamental data for the conservation of genetic diversity and germplasm resource management of E. koreanum.