Abstract:In the present study,the DNA fingerprints of Fructus Evodiae was reported.Fructus Evodiae is one of the most commercially important herbs in Guizhou Province.Amplified fragment length polymorphism(AFLP) techniques was used to analyze the DNA fingerprints of 3 types of Fructus Evodiae including Evodia rutaecarpa var.officinalis, E. rutaecarpa var.bodinieri and E. rutaecarpa(Juss.)Benth.Three primer combinations (E-AGC/M-CAG,E-AGC/M-CTG and E-ACG/M-CTG) screened out from eighteen primer pairs were used to conduct genetic analysis and variety identification of nineteen materials of Fructus Evodiae.93 bands were generated and 57 fragments appeared to be polymorphic(61.3% on average).The fragment profiles of the nineteen materials were obtained and could be distinguished from each other. The results showed that AFLP was an efficient method to identify the germplasms of Fructus Evodiae and could be a supplement for the morphological identifcation methods for Fructus Evodiae.UPGMA cluster analysis was also performed.Genetic similarity coefficient(SC) ranged from 0.235 to 0.941,indicating that Fructus Evodiae is rich in genetic diversity. Dendrogram revealed that E. rutaecarpa var.officinalis and E. rutaecarpa var.bodinieri from Yuqing region were clustered into one group,which suggested that human cultivation activities have influenced on the genetic characteristics of Fructus Evodiae.