This study investigated the pattern of genetic variation in Acacia saligna (Labill.) H.L. Wendl. to facilitate its development as a crop species for dryland salinity management. A. saligna is a morphologically variable species and four main variants are recognized. The genetic structure within A. saligna was investigated in populations across the geographic range of the species using nuclear restriction fragment length polymorphism loci. The analysis identified considerable genetic variation within A. saligna that was genetically structured into three groups. Two of the three groups corresponded to variants recognized in the field study; the third group encompassed the other two variants which, though morphologically different, were not genetically differentiated. The level of genetic differentiation between the groups suggests they may represent different taxa and a taxonomic revision of the species may be required. Identification of different taxa within A. saligna will have implications for the utilization and domestication of the species, as the taxa will need to be evaluated separately to determine their suitability for agroforestry. The high genetic variation between and within groups suggests there is a large genetic base available for breeding improved cultivars.