Abstract Hepatica insularis, a warm-temperate endemic confined to the southwestern coastal region and Jeju Island of Korea, has long posed a taxonomic challenge in relation to Hepatica asiatica, which is more broadly distributed across cool-temperate regions of northeastern Asia. To address this issue, we investigated their phylogeographical history. Genetic analyses were conducted using eight nuclear microsatellite loci and three non-coding regions of plastid DNA, based on 294 individuals sampled from 13 populations across the Korean Peninsula. Analyses of nuclear markers revealed two distinct genetic clusters concordant with geographical distribution, whereas plastid variation revealed a contrasting signal suggestive of incomplete lineage sorting (ILS). Our demographic analyses estimated that H. insularis and H. asiatica diverged approximately 17 200 years ago around the Last Glacial Maximum (LGM). The current nuclear structure probably reflects historical separation of humid coastal refugia situated along the palaeo-coastlines of the Korean Peninsula and the exposed East China Sea shelf during the LGM. Given the recency of divergence, which has resulted in ILS, we propose that these taxa do not represent distinct species, but instead reflect population-level divergence within a single species. This study sheds light on how rapid evolutionary radiation unfolds in Hepatica species and its implications for their taxonomic interpretation.