Molecular markers, whether protein or DNA-based, have become important in the study of the evolution and systematics of semi-arid legumes. Isozyme analyses have proven very valuable for the study of genetic diversity and population structure in the genera Faidherbia and Acacia. An analysis of 30 populations (approximately 900 families), from throughout the African range, of F. albida (Del.) A. Chev. have shown the occurrence of three major regions of genetic diversity: West Africa; Ethiopia/Sudan; East/South Africa. These, and other data suggest that human and animal migration patterns may have had a major influence on the distribution of Faidherbia genetic diversity in Africa. At the DNA level, RFLP analyses have been valuable for the study of genetic diversity and hybrid identification. Chloroplast DNA RFLP analysis of the neotropical legume genus Leucaena Benth. has provided valuable insights into the evolution of the genus, whilst RAPD analysis has enabled the genetic diversity of a number of species to be described. Particularly valuable in Leucaena has been a combined approach of RFLP and RAPD analyses for the identification and characterization of naturally occurring hybrids.