Abstract: Lonicera Linn. is the largest genus of family Caprifoliaceae, which has a long history and abundant resources in China. Due to its ornamental and medicinal properties, the species of Lonicera shows outstanding economic value. However, affected by the huge demand and high price stimulation, there is a serious mixing phenomenon on the market. In this study, high-throughput sequencing technology was used to analyze the analysis of L. angustifolia Wallich ex Candolle var. myrtillus (Hook. f. & Thomson) Q. E. Yang, L. myrtillus Hook. f. et Thoms. var. cyclophylla Rehd, L. szechuanica Batal and L. tangutica Maxim to sequence and assemble their chloroplast (CP) genomes, and to conduct structural comparisons and phylogenetic studies. The results showed that the chloroplast genomes of the four species showed a typical circular tetrad structure, with a total length of 154 608-163 413 bp and a total GC content of 37.93%-38.42%. A total of 128-129 genes were annotated, including 83-84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. A total of 53-68 SSRs and 133-745 long repeats were detected by chloroplast repeat structure analysis. Phylogenetic studies showed that 21 species of Lonicera medicinal plants could be significantly clustered into one branch, among which the relatives of L. angustifolia and L. szechuanica were close, and the kinship of L. myrtillus and L. tangutica was close. This study is the first comprehensive study of the chloroplast genome and phylogenetic relationship of Loicera species, and the experimental results provide a scientific basis for revealing the genetic information, species evolution and genetic diversity of Lonicera species.