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Calocedrus rupestris is listed as endangered on the IUCN Red List. In this study, we report the complete chloroplast genome (plastome) of C. rupestris. The plastome was 127,298 bp in length and encodes 118 unique genes, including 83 protein-coding genes (PCGs), 31 tRNAs, and 4 rRNAs. Nine PCGs contained one intron each and two PCGs contained two introns each. Six tRNAs contained one intron each. The overall GC content of this plastome was 34.8%. The phylogenomic analysis revealed that C. rupestris was sister to C. macrolepis and C. formosana with strong support.