Pajarete is a Chilean wine with an appellation of origin. Although it has organoleptic properties, intensive utilization of Saccharomyces cerevisiae commercial yeast through the years has presumably produced the loss of native strains that may be associated with Pajarete oenologic uniqueness. In order to evaluate the effect of re-incorporation of indigenous strains into Pajarete winemaking, native S. cerevisiae strains were isolated and selected based on their properties shown during small and large laboratory scale fermentation, and then evaluated in industrial bioreactors. From an initial set of 312 isolates, a single native strain was selected based on taxonomy, fermentation performance, aroma, residual sugars, and production of alcohol for incorporation into market scale.