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Cephalotaxus lanceolata K. M. Feng ex C. Y. Cheng W. C. Cheng and L. K. Fu (Taxaceae) is a threatened plant species and a typical plant species with extremely small populations (PSESP) with only four individuals found in Gaoligong Mountain. With the aim of providing data for future conservation efforts, we sequenced the whole chloroplast (cp) genome of C. lanceolata. The results showed that the plastid genome is 136,404 bp in size. In total, 116 unique genes were annotated, including 83 protein-coding genes, 29 tRNA genes, and 4 rRNA gen