The relationships among species in the genus Eranthis Salisb. were investigated using single nucleotide polymorphisms(SNPs) of the nuclear DNA internal transcribed spacer 1, 2 region (nrITS) and the chloroplast trn L- trn F interspacer region(cpIS). Phylogenetic relationships based on the nrITS and cpIS were inferred with posterior probabilities with STRU CTU REanalysis and the neighbor-joining method. Two major clades from nrITS and cpIS were consistent with species with yellowsepals in E. hyemalis , E. cilicica , E. longistipitata and the hybrid E . × tubergenii ; and white sepals in E. sibirica, E. longituba,E. albifl ora, E. stellata, E. pungdoensis, E. byunsanensis , and E. pinnatifi da . The phylogenetic tree of nrITS formed moresubclades than the tree of cpIS, which suggested that nrITS SNPs are useful molecular markers for phylogenetic studies in thegenus Eranthis. Only the SNPs of cpIS in E. pungdoensis accessions had a deletion at positions 259–420, and the posteriorprobability values (PPVs) assigned E. pungdoensis to population 4, which suggested that E. pungdoensis is diff erent from E. byunsanensis. Therefore, E. byunsanensis and E. pungdoensis are considered to be true-to-type based on q-values becausethe PPVs were greater than 0.9 in both species based on the STRU CTU RE analysis of nrITS SNPs. Signifi cant genetic variationin E. stellata collected in Goesan-kun and Mt. Mugap, Korea indicated a potential gene fl ow among closely relatedE. byunsanensis, E. pinnatifi da, E. sibirica, and E. stellata that could be due to geographic proximity in their distributions. E. stellata from Mt. Mugap showed mixed PPVs for E. stellata and E. byunsanensis , therefore, E. byunsanensis might be apossible hybrid origin for E. stellata collected from Goesan-kun and Mt. Mugap.