In this study, we combined data from RAD-seq, morphology, fossils, and ecological niche to understand species relationships, biogeographic history, ecological niche and morphological evolution of the blue- or white-fruited dogwoods, the largest of the four major clades of Cornus. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well-resolved phylogeny of the BW group with three intercontinental disjunct clades in east Asia/Eurasia and North America - of which two in subg. Kraniopsis are newly identified. Divergence time analyses with BEAST and treePL and DEC-based total evidence analysis resolved an ancestral range of the BW crown in eastern Asia or Eurasia in the Late Cretaceous and ancestral ranges of the three disjunct clades in Eurasia and North America during the Miocene, suggesting dispersal via the North Atlantic and Bering land bridges. Character mapping and comparison of ecological niche, morphospace, and rate of evolution shows evidence of different divergence patterns in morphology, ecological niche, and molecules of the disjunct sisters. The overall diversity bias towards EA cannot be explained by a greater net diversification rate but rather an early diversification of subg. Kraniopsis in EA. Although morphological stasis was observed in most of the characters across the disjuncts, evolutionary changes in vegetative, fruit, and habit traits may be attributed to continental differences in temperature, precipitation, and elevation. These findings in conjunction with previous studies suggest the EA-ENA disjunct floras are an assembly of lineages descended from the boreotropical or mesophytic flora through taxon-specific evolutionary pathways.