Jubaea chilensis (Molina)Baill., also named Chilean palm, is an endemic species found in the coastal area of Mediterranean sclerophyllous forest in Chile. It has a highly restricted and fragmented distribution along the coast, being under intense exploitation and anthropogenic impact. Based on 1,038 SNP markers, we evaluated the genetic diversity and population structure among six J. chilensis natural groups. We observed low levels of genetic diversity (overall HE = 0.024 and HO =0.014), a deficit of heterozygotes, and high levels of inbreeding (mean FIS = 0.424), with little or no random mating. All Wright fixation index and Nei’s genetic distance pairwise comparisons indicated moderate differentiation among populations, with a tendency to similarity. There was no evidence of isolation by distance (r =-0.214, P =0.799). In the cluster analysis, we observed a closer relationship among Culimo, Cocalán and Candelaria populations. The K value that best represented the spatial distribution of genetic diversity was ∆K =3. Habitat fragmentation and deterioration of the sclerophyllous forest may have driven inbreeding and low levels of genetic diversity in the palm groves of J. chilensis, putting the persistence of present and future populations at risk. In this scenario, it is imperative to reclassify J. chilensis as an endangered species, as well as a Natural Monument, in order to improve conservation efforts, the species management, and the environmental protection Also, the preservation of genetically different individuals may increase the overall genetic variability required to sustain the species persistence in the context of climate change and anthropogenic disturbance.