【Objective】 The purpose of the research was to explore the evolutionary pattern of chloroplast genome in the Elaeagnaceae, and in turn provide a scientific basis for species identification and resource exploitation of Elaeagnaceae. 【Methods】 This study assembled four chloroplast genomes from the species of Hippophae and Shepherdia, and compared the gene composition, repeats, and structural properties of them with those genomes previously published for plants of Elaeagnaceae. Subsequently, a phylogenetic tree was constructed based on sequences of all these chloroplast genomes. The promising sites for DNA barcoding of Elaeagnaceae were identified in the chloroplast genomes by examining the highly divergent regions. 【Results】 It was found that chloroplast genomes of each genus of Elaeagnaceae exhibited a significant degree of similarity in terms of tetrad structure, gene number and organization. Moreover, it was demonstrated that both IR regions and repeats of Hippophae and Shepherdia species tended to expand and increase more than those of Elaeagnus species. The phylogenetic tree based on chloroplast genomes from eighteen species of Elaeagnaceae showed that all plants of Elaeagnus were grouped into a branch that exhibited an early differentiation, and all plants from Hippophae and Shepherdia were classified into another branch, with a most recent common ancestry. A total of three potential DNA barcoding regions were examined in this study and the identification effect of ycf1 gene was the best. Topology of the phylogenetic tree constructed based on sequences derived from these regions were found congruent with that obtained from analyzing the whole chloroplast genomes. 【Conclusion】 This study revealed that the chloroplast genome structure of the Elaeagnus family had a conservative pattern. The IR regions and repeated sequence of the chloroplast genome have extended and increased with the evolution of Elaeagnaceae. The DNA barcoding candidates in this study exhibited strong discriminatory abilities in differentiating variations from inter-genus of Elaeagnaceae, and inter-species of Elaeagnus, as well.