A taxonomic revision and biogeographic study of the genus Centrolobium (Leguminosae - Papilionoideae) is presented. Centrolobium includes important timber trees distributed disjunctly in seasonally dry tropical forests and rain forests in Central and South America, from Panama to south-eastern Brazil. It is characterized by large samaroid pods with a spiny seed case and an abundance of orange peltate glands covering the leaves and inflorescences. Taxonomic distinctions between some species of Centrolobium have been a source of confusion. Here, seven species are recognized: C. robustum, C. microchaete, C. tomentosum, C. ochroxylum, C. sclerophyllum, C. paraense, and C. yavizanum. Previously recognized varieties of C. paraense, C. paraense var. paraense and C. paraense var. orinocense, are not maintained. Phylogenetic analysis of DNA sequence data from the internal transcribed spacer region of nuclear ribosomal DNA and the plastid matK gene and trnL-trnF intron and spacer support the monophyly of the genus. Different molecular dating methods indicate that the Centrolobium crown group and lineages found to the west and east of the Andes diverged before the Pleistocene. Divergences between species occurring east of the Andes, particularly in Bolivia and south-eastern Brazil are more recent, but nevertheless unlikely to be explained by Pleistocene climatic changes.