Daphne pseudomezereum var. koreana has traditionally been treated as a variety of D. pseudomezereum, a species endemic to the warm-temperate regions of Japan. However, var. koreana occurs primarily in cool-temperate regions of northeastern Asia— including the Baekdudaegan Mountain Range in Korea, southern Manchuria, southern Primorsky Krai, Sakhalin, and Hokkaido—and thus exhibits distinct ecological and biogeographic characteristics from var. pseudomezereum. To reassess its taxonomic position, we conducted molecular phylogenetic analyses using complete chloroplast genome and nuclear ribosomal ITS sequences. Plastome phylogeny supports var. koreana as a sister to D. kamtschatica, whereas nuclear ribosomal internal transcribed spacer phylogeny places it as a sister to var. pseudomezereum. While the phylogenetic discordance complicates its placement, we interpret this discordance as in itself ultimately revealing var. koreana as a lineage bearing an evolutionary identity possibly shaped by ancient hybridization. Evidence from ecology, biogeography, life-history (presence of well-developed rhizomes), and morphology (e.g., growth habit, calyx coloration, anther position) further supports its affinity with D. kamtschatica. Taken together, we propose reclassifying var. koreana as a variety of D. kamtschatica, representing a geographically disjunct southwestern lineage separated from var. kamtschatica by the Sea of Okhotsk. Plants occurring in southern Japan currently considered to be var. koreana may instead represent distinct, undescribed taxa.