Mortiño (Vaccinium floribundum Kunth) is a deciduous perennial shrub endemic to the high Andes of South America. Despite a rich ethnobotanic history among indigenous communities, mortiño remains a wild species vulnerable to extinction from the ongoing fragmentation of its natural habitat. This study assessed the degree of genetic diversity and population structure of Ecuadorian V. floribundum as a preliminary step towards the establishment of effective conservation and sustainable-agriculture strategies. Mortiño individuals (126 in total) sampled from 3 regions in the northern highlands of Ecuador were characterized using 11 heterologous SSR markers originally developed for Vaccinium corymbosum. Expected heterozygosity (He = 0.49) revealed a moderate degree of genetic diversity for Ecuadorian mortiño, and pairwise F statistics between sampling regions (0.019≤ Fst ≤0.041) demonstrated low-to-moderate population differentiation. Population structure analysis clustered mortiño germplasm into 3 groups, each representing the 3 distinct regions from where samples were collected. The geographic patterning of genetic diversity for V. floribundum could be explained by an isolation-by-distance model, where physical barriers along the Andean highlands reduce genetic exchange between distanced populations. To confirm the latter, this study should extend to a wider sampling range, covering other regions along the Andean alley where the species is found.