Abstract: Epimedium pinnatum Fisch. ex DC.(Berberidaceae) is a perennial herb with ornamental and medicinal value distributed in the Caucasus region. In this study, the Illumina NovaSeq 6000 sequencing system was used to assemble the complete chloroplast genome sequence of E. pinnatum for the first time. Results showed that the total length of the chloroplast genome was 156 155 bp with 38.82% GC content, comprising a large single-copy region (LSC, 89 425 bp), small single-copy region (SSC, 16 284 bp), and pair of inverted repeat regions (IRa and IRb, 25 223 bp). The chloroplast genome of E. pinnatum contained 112 genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that E. pinnatum subgen. Epimedium and sect. Macroceras was clustered on a branch, which was separated from the branch composed of species from sect. Diphyllon, subgen. Epimedium. These results suggest that further study is needed to clarify the natural system of Epimedium based on more data.