Disjunctive distribution patterns and drivers of the Sino-Japanese flora in East Asia have attracted much attention in the past decades, which is also served as an important glacial sanctuary during the quaternary glacial period. However, few studies have focused on the phylogeography, diversification and evolution of morphological character at the genus level with both nuclear and plastid data. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across China, Japan and Korea, serving as an ideal group to explore the mechanism of East Asian flora speciation and diversification. However, the phylogenetic relationships among Diabelia remain elusive and species delimitation within the genus (three species or four species) are still controversial. In this study, we reconstructed the phylogenetic relationships among Diabelia based on nuclear and cpDNA by using target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid genome trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. spathulata var. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Diabelia tetrasepala was inferred to be the result of a hybridization event from the species network analyses. The result of divergence time estimation and ancestral area reconstruction showed that Diabelia originated in Japan during the early Miocene, with subsequent gene flow between China, Japan and Korea. Overall, our results support the division of Diabelia into five main clades and this research provides new insights for the speciation process and taxonomy within Diabelia.