A new putative species of $Pulsatilla$, $P.$ $tongkangensis$ Y. Lee et T. C. Lee, growing in calcified rock cavities was discovered along the Donggang, Jeongseon-gun, Gangwon Province, Korea. Accessions of $P.$ $tongkangensis$ and $P.$ $koreana$ (Y. Yabe ex Nakai) Nakai ex T. Mori were characterized with randomly amplified polymorphic DNA (RAPD) markers and single nucleotide polymorphisms (SNPs) of the chloroplast $trnQ$, $trnH$, $psbA$ genes and the $atp$B-$rbc$L intergenic spacer regions. $Pulsatilla$ $tongkangensis$ exhibits significant morphological variation in leaf morphology, and flower color (white, purple blue, to light red), and flower bud orientation (lateral-facing to up-facing). Two data sources were used: RAPD analysis and SNPs of chloroplast DNA (cpDNA) from accessions collected from the native sites and with progeny from controlled pollination between $P.$ $tongkangensis$ and $P.$ $koreana$. One $P.$ $tongkangensis$ accession with light-red flowers was clustered with $P.$ $koreana$ in dendrograms using RAPD markers, and three accessions of $P.$ $tongkangensis$ with pink-blue narrow petals, light-blue narrow petals, and white petals had the same SNPs as $P.$ $koreana$. A species-specific RAPD band for each $P.$ $tongkangensis$ and $P.$ $koreana$ was identified, and both bands were present in some $P.$ $tongkangensis$ accessions collected from Mt. Backwoon, indicating that these were of hybrid origin. The presence of species-specific bands and variations in SNPs suggest that significant genetic variation exists and that variation resulted possibly from cross pollination and introgression between these two closely related species. Based on the results of these studies, it is suggested that $P.$ $tongkangensis$ is a heterogeneous population resulting from the introgression due to cross-pollination with $P.$ $koreana$. A discussion is presented to reconsider the taxonomic treatment of $P.$ $tongkangensis$ as a new taxon based on the modern concepts of species.