AbstractCotinusis an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy ofCotinuswas mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced the chloroplast (cp) genomes of all currently recognized taxa ofCotinus, including three species and four varieties. A comparative analysis was performed to investigate their cp genome characteristics and evolution. Furthermore, we inferred the phylogenetic relationships ofCotinusbased on whole cp genomes, protein‐coding genes, and nuclear ITS data. All cp genomes exhibited a typical quadripartite structure with genome sizes ranging from 158,865 to 160,155 bp. A total of 113–114 genes were identified in the genomes. Seven non‐coding and four coding regions were identified as the most divergent hotspots for potential molecular barcodes and phylogenetic markers. Selection pressure analysis showed that there had been positive selection on genesmatKandrps8in theCotinuscp genomes. Phylogenetic results confirmed thatCotinusis a monophyletic group but the widely distributed speciesCotinus coggygriais not monophyletic. The divergence‐time analysis suggested thatCotinusunderwent an evolutionary divergence from the middle Eocene and rapid adaptive radiation from the middle Miocene. This study revealed new insights into the cp genome evolution and phylogeny ofCotinusand related taxa.