Conservation and sustainable management of lineages providing non‐timber forest products are imperative under the current global biodiversity loss. Most non‐timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus <jats:italic>Parajubaea</jats:italic> (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, <jats:italic>P. torallyi</jats:italic> and <jats:italic>P. sunkha</jats:italic>, are non‐timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, <jats:italic>P. cocoides</jats:italic>, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of <jats:italic>Parajubaea</jats:italic> species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low‐copy nuclear genes (3753 bp) challenged the hypothesis that <jats:italic>P. cocoides</jats:italic> is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single‐nucleotide polymorphism markers by genotyping‐by‐sequencing of 194 wild <jats:italic>Parajubaea</jats:italic> individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
