Total DNA was extracted from the leaves of seven Epimedium species grown in different places in Japan. Their genetic characterization was performed by DNA analyses of random amplified polymorphic DNA (RAPD) using 32 random primers having 10 base sequences, and by restriction fragment length polymorphism (RFLP). E. sagittatum and E. koreanum were easily distinguished by a representative amplified band pattern. It became evident that E. sagittatum had extremely different genetic composition compared to the other species. A dendrogram obtained from the similarity matrix by cluster analysis indicates that E. sagittatum can be completely isolated from the other species. Moreover, it became evident that E. grandiflorum var. higoense, E. trifoliatobinatum and E. koreanum are independent species, contrary to the previous assumption that they are subspecies or a variety. The geographical variation of E. sempervirens was confirmed by cluster analysis. E. diphyllum showed wide genetic variations, in spite of sampling from the same area.