Hepatica insularis Nakai, a perennial herb endemic to warm-temperate regions on the Korean Peninsula, has been a subject of taxonomic debate due to its morphological similarities with Hepatica asiatica Nakai. To address the taxonomic ambiguity and provide evolutionary insights into H. insularis, we developed 15 polymorphic microsatellite markers. Of these, eight markers were successfully cross-amplified in H. asiatica, demonstrating their broader applicability. The markers exhibited high levels of polymorphism, with the number of alleles per locus ranging from two to eleven. The expected heterozygosity (H<sub>E</sub>) and observed heterozygosity (H<sub>O</sub>) values ranged from 0.180 to 0.802 and from 0.000 to 0.933, respectively. The developed markers will serve as a valuable tool for future phylogeographic studies aiming to understand the genetic structure and diversity of H. insularis and related taxa.