The genus Dalbergia has a pantropical distribution and comprises approximately 250 species. Previous phylogenetic studies on the genus revealed that Dalbergia is monophyletic and is sister to Machaerium and Aeschynomene sect. Ochopodium. However, due to limited samples or DNA regions in these studies, relationships among the major clades are still unresolved, and divergence dates and biogeographical history of the genus have not been addressed. In this study, phylogenetic analyses of Dalbergia were conducted using broad taxon sampling and a combined dataset of two plastid DNA markers (matK and rbcL) and one nuclear marker (ITS). We evaluated the infrageneric classification of the genus based on the reconstructed tree, and investigated biogeographical history of this genus through molecular dating and ancestral area reconstruction analyses. The monophyly of Dalbergia was strongly supported and the genus was resolved into five major clades with high support, several of which correspond to the previous recognized sections. We inferred that Dalbergia originated in South America during the Early Miocene (c. 22.9 Ma) and achieved its current pantropical distribution through multiple recent transoceanic long-distance dispersals (LDD). We highlighted the important historical events which may explain the pantropical distribution pattern of Dalbergia.