Objective: To assess the population genetic diversity and genetic structure and screen species - specific bands for i-dentification of Changium smyrnioides and Chuanminshen violaceum. Method: Seven wild populations of Changium smyrnioides and one cultivated population of Chuanminshen violaceum were studied by ISSR analysis. The population genetic diversity and population genetic structure were assessed by using POPGENE software. Result: A total of 152 ISSR markers were scored, among which 136 (90. 8%) were polymorphic. The values of Gst tended to be high (mean Gst = 0. 575). The level of genetic diversity of Changium smyrnioides (A = 1.272; P = 27. 26 % ; I = 0. 132;H = 0.087)was higher than that of Chuanminshen violaceum (A = 1.217;P = 21.7;I = 0.103;H = 0. 067). Conclusion: The genetic variation of Changium smyrnioides is high and the majority of genetic variation occur among populations. Substantial genetic divergence is shown by cluster analysis (UPGMA) to befound between Changium smyrnioides and Chuanminshen violaceum at DNA level. In addition, one species-specific marker has been obtained in Chuanminshen violaceum . The phylogenetic relationship of two species has also been discussed.