Understanding the causes of the Sino‐Japanese disjunctions in plant taxa has been a central question in eastern Asian biogeography, with vicariance or long‐distance dispersal often invoked to explain such patterns. Diabelia Landrein (Caprifoliaceae; Linnaeoideae) comprises four shrubby species with a Sino‐Japanese disjunct distribution. The species diversification time within Diabelia, covering a long geological history of the formation process of the Sino‐Japanese flora, dated back to the middle Oligocene, therefore, Diabelia would be an ideal model to elucidate the biogeographic patterns of Sino‐Japanese disjunctions with climate fluctuation. In this study, we analyzed complete plastome sequence data for 28 individuals representing all four species of Diabelia. These 28 plastomes were found to be highly similar in overall size (156 243–157 578 bp), structure, gene order, and content. Our phylogenomic analysis of the plastomes supported a close relationship between Diabelia ionostachya (Nakai) Landrein & R.L. Barrett var. wenzhouensis (S.L. Zhou ex Landrein) Landrein from eastern China and Diabelia spathulata (Siebold & Zucc.) Landrein var. spathulata from Japan. Diabelia serrata (Siebold & Zucc.) Landrein was identified as sister to a population of Diabelia sanguinea (Makino) Landrein from Tochigi in central Japan and D. spathulata Landrein, from Toyama, central Japan. Most Diabelia lineages were estimated to have differentiated 8–28 Mya. Our results indicate that two independent vicariance events could explain the disjunction between Japan and Korea in the mid to late Miocene, and between Zhejiang and Japan in the early Miocene.