Daphne pseudomezereum A. Gray var. koreana (Nakai) Hamaya is a shrub distributed in high mountains in Japan and Korea and is used as a medicinal plant. The complete chloroplast genome of D. pseudomezereum var. koreana is 171,152 bp long with four subregions consisting of a large single-copy region (84,963 bp), a small single-copy region (41,725 bp), and a pair of inverted repeats (2739 bp). The genome includes 139 genes (93 protein-coding genes, eight rRNAs, and 38 tRNAs). Phylogenetic analyses show that D. pseudomezereum var. koreana is nested within the Daphne clade in the narrow sense and that it forms a distinct lineage.