Abstract:The genetic relationship of M. ruthenica populations were analyzed from seven provinces of China by ISSR marker. 16 primers with strong polymorphism and good repeatability were screened from 80 ISSR primers. Amplification of 44 populations M. ruthenica genomic DNA ,133 bands were amplified, an average of each primer amplified 8.31 bands, of which (115 bands)87.08% were polymorphic. The genetic dissimilarity coefficients of M.ruthenica germplasm ranged from 0.436 to 0.908. 44 populations M. ruthenica germplasm were divided into eight groups with the higher correlation of geography resource by UPGMA cluster analysis.