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Disanthus cercidifolius subsp. longipes is a rare and endangered plant species. In our study, the complete chloroplast genome was assembled by using high-throughput DNA sequencing data. The whole CP genome is 158,076 bp in length, comprising of a large single-copy region of 87,148 bp, a small single-copy region of 18,300 bp, and two inverted repeat regions of 26,314 bp each. There are 136 genes in the genome, including 86 protein-coding genes, 40 transfer RNA genes, eight ribosomal RNA genes, and two pseudogenes (ndhK and ycf1). Phylogenetic results demonstrated that D. cercidifolius subsp. longipes grouped with other Hamamelidaceae species, with a support rate of 100%.