Abstract:In order to investigate the genetic diversity and relationship of genus Epimedium in Sichuan province, 7 species including 12 populations were used to study the genetic variation by the ISSR marker technique. The result showed that 194 DNA fragments among 12 populations were amplified using 23 reliable ISSR primers, among which 169 DNA bands were polymorphic (the percentage of polymorphic bands reached 87.11%). The genetic distance and similarity among 12 populations were 0.298 0-0.620 7 and 0.653 2-0.748 9, indicating variation of genetic diversity existed among different populations. The observed effective number of alleles (Ne), Nei’s gene diversity index (He) and Shannon’s information index (I) were 1.534 2, 0.314 4 and 0.469 7, respectively, showing the geographical distribution was very obvious. The result of cluster analysis using the unweighted pairgroup method with arithmetic average (UPGMA) and Principal Component analysis (PCA) based on ISSR data both showed that these tested resources were divided into two main groups. In addition, the ISSR marker technique is suitable for the analysis of the genetic diversity and relationship of genus Epimedium in Sichuan.