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Heracleum yungningense is a traditional medicinal plant widely used in China. Here, we reported the complete chloroplast genome of H. yungningense using Illumina paired-end sequencing. The whole genome is 149,223 bp in length, which contains a pair of 18,496 bp inverted repeats regions separated by a large single-copy region and a small single-copy region with 94,770 bp and 17,461 bp in length, respectively. Additionally, the cp genome of H. yungningense contains 113 genes, including 80 protein-coding genes, 29 transfer RNAs, and 4 ribosomal RNAs. The GC content of this cp genome is 37.5%. Phylogenetic analysis was conducted to assess inter-relationships among the major clades of Apiaceae, which strongly supported the close relationship of H. yungningense and H. moellendorffii.