Object: The genus Hippophae comprises of several important medical species which widely used in traditional Chinese medicine (TCM) and Tibetan medicine.Due to the morphological similarity and the most commonly used forms, many dried fruits from other species of Hippophae have been used to alternate the medicinal species it brings lots of difficulties to distinguish Hippophae species from each other.This may seriously affected its clinic effect and quality control.This study aims to evaluate the suitability and feasibility of the empirical DNA barcodes for discrimination of medicinal Hippopahe species.Methods: Two single locus regions,internal transcribed spacer 2 (ITS2), psbA-trnH and a combination (ITS2+ psbA-trnH)were tested for identification of 7 species and 11 subspecies in Hippophae.Detection of the kimura 2-parameter (K2P) distance,the neighbor-joining (NJ) tree and barcoding gap were used to assess the identification efficiency.Results: DNA was successfully extracted from the dried fruits samples.Amplification and sequencing efficiencies for both ITS2 and psbA-trnH were 100%.On analyzing the sequence data, combination of multiple markers ITS2+ psbA-trnH proved to be the most suitable candidate barcode at the species and subspecies level, all 7 species and 4 subspecies in Hippophae could be effectively differentiated based on NJ tree method; only one species distributed in no barcoding gap area.Conclusion: The ITS2 combined with psbA-trnH is an ideal DNA barcode that can be used as a powerful tool for the identification of Hippophae.