AbstractSimilar to the global phenomenon, many plant species endemic to Korean limestone karst forests are at risk of extinction due to human intervention.Zabelia tyaihyoniiis a familiar shrub, called “Hardy abelia” and “Fragrant abelia” growing in the karst forests of Korea, where it is one of the most threatened species. We investigated the genetic structure and demographic history ofZ. tyaihyonii, which allow us to develop appropriate conservation and management strategies. The genetic structure was evaluated using a total of 187 samples from 14 populations, covering the entire distribution ofZ. tyaihyoniiin South Korea. We utilized 254 and 1753 SNP loci obtained via MIG‐seq (Multiplexed ISSR Genotyping by sequencing) for structure and demographic analyses, respectively. The population demographic modeling was performed with site frequency spectrum. To gain further historical insights, we also employed ENM (Ecological Niche Modeling). We found two distinct clusters (CLI and CLII) of ancient origin (ca. 490 ka). Despite CLII experiencing a more severe bottleneck, both clusters showed similar levels of genetic diversity, indicating mutual historical gene flow. Their historical distribution range seems to have changed very little. We proposed a historical distribution scenario forZ. tyaihyonii, taking into account its intrinsic factors, and emphasized a more complex response to Quaternary climate change beyond simple allopatric speciation models. These findings provide valuable insights for conservation and management strategies forZ. tyaihyonii.