Use of saline lands for agroforestry relies primarily on plant species that have the trait of salinity tolerance, and also other economic and agronomic benefits. The selection of species, however, also needs to consider other key factors such as compatibility with existing flora, and potential for environmental benefits such as improved soil fertility or lowering of the water table in the case of dryland salinity. The testing of candidate species in particular environments needs substantial investments of costs and time. In this paper, a novel approach is presented for the rapid identification of potentially salt tolerant Acacia species, based on molecular phylogenetic analysis. The approach has been applied to four species groups, Acacia pendula, A. salicina, A. victoriae and A. stenophylla. The nuclear-encoded ribosomal DNA internal and external transcribed spacer (ITS and ETS) regions were used as markers, and phylogenetic analyses undertaken to identify closely related species that may share the salt tolerance traits. Such a methodology could be used to more rapidly identify candidate native species for agroforestry in salinity-affected regions and for preventing further expansion of salinity, thus assisting in biodiversity conservation.