[Objective] In order to clarify the structural features of the chloroplast genome of Berberis diaphana and the phylogenetic relationship with the taxa of the same genus, we comprehensively analyzed its chloroplast genome structure characteristics and phylogenetic. [Methods] Sequencing was performed by Illumina Hiseq X Ten technology, and the chloroplast genome characteristics of Berberis diaphana were analyzed by using CPGview, CodonW, MISA, Reputer, IRscope, and mVISTA software, and phylogenetic tree was constructed by ML method in MEGA7 software. [Results] The results showed that the chloroplast genome of Berberis diaphana have a length of 166 225 bp, with a typical quadripartite structure and the GC content of the whole genome was 38.07%. A total of 144 genes were annotated, including 99 protein coding genes, 37 tRNA genes, and 8 rRNA genes. Among them, 23 genes contained introns, and 32 genes were present in duplicate copies. Preference for codons ending in A/U. A total of 98 SSR loci and 150 scattered repeat sequences were detected, and most SSR loci composed of A/T bases. The degree of variation in the SSC and IR regions was higher than that in the LSC region. Phylogenetic analysis revealed that Berberis diaphana was most closely related to Berberis weiningensis. [Conclusion] The chloroplast genome structure characteristics of B. diaphana are similar to other species of berberis, which can serve as a theoretical basis for studies on chloroplast genetic engineering, genetic diversity analysis, molecular breeding, and species identification.