Abstract: Despite the high economic and ecological value of Hippophae, which possesses rich economic and ecological benefits, research on the taxonomy and phylogenetics of Hippophae remains insufficient and controversial. This study is based on an examination of the chloroplast genomes of two Hippophae species— Hippophae tibetana and Hippophae neurocarpa — with the aim of investigating their phylogenetic and taxonomic relationships. After sequencing and assembling, the genome sizes of Hippophae tibetana and Hippophae neurocarpa, were determined to be 155 810 bp and 156 316 bp, respectively. The difference in（G+C） content between the two types was only 0.02 percents. Through annotation, it was revealed that both Hippophae tibetana genome and Hippophae neurocarpa genome contain 131 and 132 genes, along with 246 and 247 simple sequence repeats, and 41 and 36 long sequence repeats, respectively. Six highly variable regions were identified in the chloroplast genome of Hippophae, which can be utilized for phylogenetic analysis and the development of molecular markers. The resulting phylogenetic tree indicates that Hippophae tibetana forms a distinct clade, while Hippophae neurocarpa and subspecies of Hippophae such as Hippophae rhamnoides subsp.monglica are grouped together in another clade. This investigation will serve as a foundation study for understanding the taxonomy and phylogeny of Hippophae.