Drylands are one of the most vulnerable ecosystems on the earth. Agricultural production from these areas is minimal due to prevailing hostile environment, and most of the land remains underutilized. This fragile ecosystem is further weakened by periodic droughts and increasing overexploitation of the meager resources. The growth of woody leguminous species is full of promise in such areas due to their nutritional, economic, and ecological characteristics. Acacias are legumes that have aided in the recovery of marginal lands for agricultural development due to their ability to fix atmospheric nitrogen controlling soil erosion, providing refuge for other species, improving soil mineral composition and microbial biodiversity, in addition to being an important source of food in desert ecosystems. Sustainable use of these species are however, hampered by the continual deforestation, habitat fragmentation and progressive climate change. Knowledge about the status and trends of species genetic diversity provides a basis for their conservation and maintenance. Owing to the technological advancement and their ever reducing costs, molecular markers provide ways to identify species or describe genetic variation of populations that can be used for gene conservation and restoration programs. In this communication, we review advances in the development and application of molecular markers in conservation, planning, landscaping and restoration of Acacia species with reference to drylands and discuss future prospects.