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In order to supply genetic information of Juniperus saltuaria, we reported the complete chloroplast genome sequence based on high-throughput sequencing data. The whole chloroplast genome was 128,099 bp long with an asymmetric base composition (32.9% A, 16.9% C, 18.1% G and 32.1% T). The genome annotation predicted a total of 116 genes, including 82 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The neighbor-joining phylogenetic analysis based on 45 complete chloroplast genome sequences showed that J. saltuaria was more closely related to the congeneric J. recurva. The assembled chloroplast genome of J. saltuaria will provide useful genomic data both for the phylogenetic research of Juniperus and the conservation of this species.