| Summary: | Capparis versicolor Griff. is a rare and threatened medicinal plant in South China. Chloroplast (cp)-derived markers have been widely used to study evolutionary relationships of many species. In this study, the complete cp genome of C. versicolor was assembled based on next-generation sequencing. The whole genome was 155,051 bp in length, consisting of a pair of inverted repeats, large single copy region, and a small single copy region. The cp genome contained 123 genes, including 83 protein-coding genes, 4 rRNA genes, and 36 trRNA genes. The overall GC content of the whole cp genome was 36.38%. A neighbour-joining phylogenetic analysis demonstrated that C. versicolor is clustered together with Pachycladon enysii.
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