Senegalia is a genus of the legume family (Leguminosae: Mimosoideae) that has a pantropical distribution with centers of diversity in Brazil, Mexico and southern Africa. The genus is characterized by plants having bipinnate leaves, presence of petiolar nectaries, prickles on the branches, and pollen grains arranged in polyads with 16 grains. Morphology is an important tool for identification of Senegalia species, but it is not sufficient to resolve all taxonomic issues and elucidate the evolutionary history of this genus. Prior molecular analyses of Mimosoideae have lacked breadth of sampling within Senegalia, leaving many relationships uncertain, particularly the relationship among Brazilian species and other members of the genus. The aim of this study was to identify Senegalia s. s. lineages that contain Brazilian species, and to investigate the relationship of these species with non-Brazilian Senegalia species. We present the first comprehensively sampled phylogeny of American and African Senegalia, however Asian species are not sampled. We sequenced four plastid and one nuclear DNA (ITS) regions for 125 samples of 59 Senegalia and one Parasenegalia species. Both Bayesian and maximum likelihood analyses were performed. Neither the American or African species form monophyletic lineages. The lack of monophyly of these groups suggests a more complicated evolutionary history of the genus than previously considered, including probable transatlantic dispersal events.