Technical Abstract: Microsatellites are molecular markers with great potential for investigating genetic structure of populations. This information is valuable for generating effective conservation plans. We studied the endemic and endangered Phaedranassa viridiflora (Amaryllidaceae) to show the utility of microsatellite markers for conservation purposes. Phaedranassa viridiflora is the only species of the genus with yellow flowers. Our results provided the first evidence of natural hybridization between P. viridiflora and P. dubia in northern Ecuador, at Pululahua crater. The central-southern populations do not show hybridization with other species of the genus. Genetic diversity was highest in the Pululahua population. Central and southern populations have a higher proportion of clones than Pululahua. Bayesian and cluster analysis suggest that the yellow flower type evolved at least three times along the Ecuadorean Andes. The results of this study show that microsatellite markers are a valuable tool to estimate genetic diversity patterns.