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Torreya grandis var. jiulongshanensis (Taxaceae) is an evergreen tree endemic to Zhejiang province, China, and it is listed as a rare plant species with extremely small populations. In our present study, we assembled the chloroplast (CP) genome of T. grandis var. jiulongshanensis using high-throughput sequencing data generated by an Illumina Hiseq X Ten platform. The results indicate that the complete CP genome is 136,705 bp in size with an overall guanine and cytosine content of 35.5%. The plastome has lost its quadripartite structure. In the CP genome, there are a total of 119 genes, including 82 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes. Phylogenetic analysis revealed that T. grandis var. jiulongshanensis is a sister species to T. grandis.