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Objective: To identify the plants in Vitex including Vitex negundo L. , V. negundo var. cannabifolia (Sieb. et Zucc. ) Hand.-Mazz. , V. trifolia L. and V. trifolia L. var. simplicifolia Cham.. Methods: Both intra- and inter-species relationships among these plants were analyzed by RAPD marker. Twenty-one samples collected from different locations in China were tested using 25 RAPD arbitrary 10-mer primers which were screened from 32 primers. Cluster analysis was conducted by Wards minimum variance method of SAS software. Results: A total of 224 bands were produced and 128 bands showed polymorphism among 21 samples. The level of polymorphism within species was 51.7％. The dendrogram constructed based on RAPD analysis showed that 21 samples can be placed in 2 groups at the level of SPRS value of 0. 3636. The first group included V. trifolia var. simplicifolia and V. trifolia. The other consisted of V. negundo and V. negundo var. cannabifolia.. At the level of SPRS value of 0.1, 21 samples canbe obviously divided into 3 groups. V. trifolia and V. trifolia var. simplicifolia were clustered into one group, V. negundo and V. negundo var. cannabifolia were separately clustered to 2 groups. Conclusion: RAPD analysis is in good agreement with the traditional plant taxonomic classification, and fundamentally identical with their origins and morphologic characteristics, which indicates that the genetic relationship a mong samples is related to their center of origin. These medicinal species in Vitex have their specific bands which are available to identify. These specific bands can be used as species-specific molecular markers of Fructus Viticis for the application of germplasm identification and classification.