The genus Vachellia Wight & Arn. has a pantropical distribution, with species being distributed through Africa, the Americas, Asia and Australia. The relationships among the lineages from Africa and America are well understood, but the phylogenetic placement and evolutionary origins of the Australian species of Vachellia are not known. We, therefore, sequenced four plastid genes from representatives of each of the nine Australian species of Vachellia, and used Bayesian inference to assess the phylogenetic placement of these lineages, and a relaxed molecular clock to assess the timing of diversification. The Australian species of Vachellia form a well-supported monophyletic clade, with molecular-dating analysis suggesting a single dispersal into Australia 6.5 million years ago (95% range 13.9–2.7 million years ago). Diversification of the Australian clade commenced more recently, c. 3.1 million years ago (95% range 9.2–1.2 million years ago), perhaps driven by the increased aridification of Australia at this time. The closest relatives to the Australian Vachellia were not from the Malesian bioregion, suggesting either a long-distance dispersal from Africa, or two separate migrations through Asia. These results not only improve our understanding of the biogeography of Vachellia species, but also have significant implications for the biological control of invasive Vachellia species in Australia.