The Azapa Valley (Arica, Chile) exhibits severe native forest fragmentation as a result of intensive agricultural expansion, threatening the chañar (Geoffroea decorticans, Fabaceae), a critical habitat for the critically endangered Chilean woodstar (Eulidia yarrellii). In this study, the fine scale spatial genetic structure (SGS) and dispersal distance were evaluated based on 9 microsatellite loci and the spatial coordinates of the sampled trees (n = 42). The SGS in this G. decorticans population from the Azapa Valley was high (Sp = 0.058), similar to that observed in other highly fragmented forest species. Particularly, the structure was significant only at short distances, showing a high initial kinship coefficient (F1 = 0.21) and a significant negative regression slope (blog = -0.046; P < 0.001), indicating a clear restriction in pollen and seed dispersal. The estimated neighborhood size was small (Nb = 17.18 individuals), and the gene flow dispersal distance ranged between 19.5 and 23.4 meters according to local density (0.0036 and 0.0025 ind/m2, respectively), reflecting the non-homogeneous distribution in the area. These results demonstrate that gene flow in chañar occurs at highly local scales, confining remnant populations to clusters vulnerable to inbreeding. In conclusion, to ensure genetic diversity and resilience in this desert oasis, germplasm collection radii for active restoration programs must exceed the detected biological dispersal distances.