Resolving phylogenies among closely related species remains a perplexing problem in plant systematics. All too often cpDNA and nrDNA ITS are insufficiently variable to provide desired resolution or support. In the present study, we have adopted a RAPD-based approach to develop sequence-characterized regions, from the nuclear genome, with levels of DNA sequence variation appropriate for resolving relationships within subclades of Leucaena (Fabaceae). RAPDs were used to amplify a set of seven Leucaena accessions. Equal length fragments amplified in two or more species were sequenced and compared. Specific primers were designed for aligned product sets displaying similar or greater levels of variation than have been found in previous ITS studies. Two regions whose DNA sequences provided greater resolution and bootstrap support than ITS or cpDNA RFLP restriction site data sets for the same sample of Leucaena species are discussed in detail.