Natural hybridization is frequent in plants and is considered an important factor facilitating speciation. The natural intergeneric hybridization between Ligularia and Cremanthodium was previously confirmed using a couple of DNA markers. However, the mechanism of this intergeneric hybridization and the role of reproductive isolation in the process of hybridization remain unclear. Here we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to further quantify the occurrence of hybridization, the genetic structure of the hybrid population and the role of reproductive isolation between Ligularia nelumbifolia and Cremanthodium stenoglossum. The results based on the ddRAD-seq SNP data sets indicated that hybridization between L. nelumbifolia and C. stenoglossum was restricted to F1s, and no gene introgression was identified between these two species. STRUCTURE analysis and maximum likelihood (ML) tree results showed a slightly larger genetic contribution of L. nelumbifolia to putative hybrid F1s. We deduced that the reproductive isolation between these two parent species is not well-developed but still strong enough to maintain the genetic integrity of the species, and that their F1s are sterile or with low fertility. Given the poorly resolved phylogenetic relationship between Ligularia and Cremanthodium, the occurrence of natural hybridization between L. nelumbifolia and C. stenoglossum may provide new insights into the re-circumscription and re-delimitation of these two genera.