Mangata, the Desert Quandong Santalum acuminatum, is an iconic bush food species that is highly valued for its ecological importance and cultural significance. In Central Australia, ensuring long-term persistence of Mangata includes management for recurrent fire and Buffel grass, browsing, trampling and drought impacts to maintain wild populations and build resilience. Furthermore, augmentation is an identified recovery action that can support desires to have this bush tucker species thriving again. Selecting source sites to collect fruits and seed for growing is a key consideration. Conservation efforts and integrated management can be guided by genetic information about Mangata, including selecting beneficial source sites for translocation and protecting priority populations for species recovery. Findings from population genetic research on Mangata in the Northern Territory clarify guidance for conserving priority sites including Watarrka National Park and Uluru-Kata Tjuta National Park. Through applying a targeted Single Nucleotide Polymorphism panel of genetic markers specific to Mangata, we identify two genetic lineages in Central Australia. I highlight implications of this genetic variation to protecting source stands and evolutionary persistence in Central Australia; identify sites for seed collecting for cultivation on Parks likely to benefit wild stand survival through gene flow; and discuss collaborative conservation and management for Mangata.