Pseudophoenix ekmanii is a threatened palm species endemic to the Dominican Republic. Sap from trees is extracted to make a local drink; once they are tapped the individual usually dies. Plants are also illegally harvested for the nursery trade, and destroyed by poachers hunting the endemic and threatened Hispaniolan parrot. We used seven DNA microsatellite markers to assist land managers in developing conservation strategies for this palm. We sampled four populations along the known distribution range of this species (three populations from the mainland and one from the small island of Isla Beata), for a total sample of n=104. We found strong evidence for genetic drift, inbreeding, and moderate gene flow (i.e., all populations had at least four loci that were not in Hardy Weinberg Equilibrium, at least nine loci-pairs were in Linkage Disequilibrium, the pair-wise FST values ranged from 0.069 to 0.266, and had positive FIS values). Data supported an isolation-by-distance model, and cluster analyses based on genetic distances resolved two groups that match a north-south split. The population from Isla Beata had the lowest levels of genetic diversity and was the only one in which we found pairs of individuals with identical shared multi-locus genotypes.