The genus Cynometra (Leguminosae, Detarioideae) is a large, pantropical group of woody plants ranging in size from 5-50 meters. While many recent advances have been made in higher level legume systematics, many large genera still require more study to test their monophyly. Further, its relationship to the much smaller Pacific genus Maniltoa is unclear. Here we present the first broadly-sampled phylogeny of Cynometra and Maniltoa, based on molecular data from three chloroplast loci: matK, the trnL intron and the trnL intergenic spacer. Our analyses indicate that Cynometra is not monophyletic as currently circumscribed, as several researchers had previously suspected. We recover two strongly supported clades of Cynometra sensu lato; one that is most closely related to a clade consisting of the genera Dicymbe and Polystemonanthus and is composed of exclusively African taxa and another clade that is pantropical and is nested in a larger clade with the Scorodolphoeus group and the genera Normandiodendron, Neochevalierodendron, and Zenkerella. Futhermore, the genus Maniltoa is nested within the pantropical Cynometra clade and is also non-monophyletic. The two clades are each supported by several morphological characters that can be used to distinguish between them (e.g. inflorescence structure, pedicel articulation, fruit dehiscence). These results will be used to modify the classification by moving the relevant African taxa to a new genus and placing Maniltoa in synonymy with Cynometra.