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Coptis is one of the most important medicinal plant genera in eastern Asia. To better understand the evolution of this genus, the complete chloroplast genome of C. chinensis var. brevisepala was obtained by next-generation sequencing. The plastome of C. chinensis var. brevisepala is 155,426 bp in length, and consists of large (LSC, 84,488 bp) and small (SSC, 17,402bp) single-copy regions, separated by pair of inverted repeat regions (IRs, 26,768 bp). It harbours 111 unique genes, including 78 protein-coding genes, 29 transfer RNA genes, and four ribosomal RNA genes. Rps19 and ycf1 were pseudogenized due to incomplete duplication in IR regions. The nucleotide composition is asymmetric (30.5% A, 19.4% C, 18.7% G, and 31.3% T) with an overall G + C content of 38.2%. The phylogeny of Ranunculaceae based on 75 CDSs of 27 taxa showed that Ranunculoideae is paraphyletic and thus needs redefinition.