Abstract:Juniperus sabina was used as material, highthroughput sequencing technology was used to sequence the chloroplast genome of J. sabina, and the structural characteristics and phylogenetic relationships of J. sabina chloroplast genome were analyzed. The results showed that:(1)J. sabina chloroplast genome was 157 739 bp in length, consisting of a large singlecopy region, a small singlecopy region and the two inverted repeat regions with only 261 bp. The cpDNA of J. sabina contains 119 genes including 82 proteincoding genes, 4 rRNA genes and 33 tRNA genes. The trnICAU and trnQUUG genes have two copies, but only trnQUUG is located in the IR region while the other genes are singlecopy genes. (2)Bioinformatics analysis showed that there were 42 579 codons in the chloroplast genome of J. sabina, of which Leu was the most abundant one, and AGA/UUA was the most highly used relative codon. A total of 47 SSRs were predicted in the chloroplast genome of J. sabina. The number of single nucleotides, dinucleotides, and trinucleotides was 38, 1, and 3, respectively; The genome size, genetic composition, and GC content of J. sabina were similar to other junipers. (3) The RAxML software was used with maximum likelihood method to construct phylogenetic tree for a total of 31 species of plants, such as Salicaceae, Pinaceae, Rosaceae and Cypress. The results showed that J. sabina has a closer relationship with Juniperus bermudiana and all juniper species form a monophyletic group. The study provided a theoretical basis for enriching the genetic resources of J. sabina for the evaluation and conservation of J. sabina germplasm resources, molecular breeding, development of SSR molecular markers, genetic diversity and phylogeography of population, also provided support for the systematic evolution of J. sabina.