Gliricidia sepium provides a variety of products important for rural communities in tropical countries. Native populations in Meso-America currently form an important source of seed for distribution to farmers, but concerns centre on mechanisms which may lead to their genetic erosion, including anthropogenic dispersal and subsequent introgression from the related species, G. maculata. Populations of Gliricidia were examined genetically using approaches based on the polymerase chain reaction to test for interspecific hybridization and introgression between G. sepium and G. maculata. Analysis involved 13 RAPD and two RFLP-PCR markers which were identified to have species-diagnostic distributions. Data from both approaches corresponded and indicated three locations where multilocus genotypes were consistent with an hybrid origin. Data at one of these sites was consistent with introgression following hybridization. The hybrid origin of populations was supported by the intermediate geographical location of these sites to 'pure' populations of each species. Analysis of maternally inherited organellar DNA, which involved the detection of SSCPs in mitochondrial DNA amplification products, allowed further delineation of genetic structure among Gliricidia populations. Mitochondrial data indicated a high degree of organelle differentiation between sampled locations and identified G. sepium- and G. maculata-diagnostic haplotypes. This data supported the interpretation of genetic structure based on RAPDs and RFLP-PCR. In addition, cytonuclear analysis allowed the directionality of gene transfer during the formation of hybrid populations to be described. Despite evidence for the occurrence of interspecific hybridization and introgression in Gliricidia, important resource populations of G. sepium on the Pacific coast appear to have retained their genetic integrity. Implications in terms of the conservation and utilization of genetic resources within the genus are discussed.