AimsIn order to improve the quality and to create a biological basis for obtainment of the protected denomination of origin (PDO), indigenous yeast were isolated and characterized for use in Salinas city (the Brazilian region of quality cachaca production). Material and methodsSeven thousand and two hundred yeast colonies from 15 Salinas city distilleries were screened based on their fermentative behaviour and the physicochemical composition of cachaca. Molecular polymorphic analyses were performed to characterize these isolates. ResultsTwo Saccharomyces cerevisiae strains (nos. 678 and 680) showed appropriate characteristics to use in the cachaca production: low levels of acetaldehyde and methanol, and high ethyl lactate/ethyl acetate ratio respectively. They also presented polymorphic characteristics more closely related between themselves even when compared to other strains from Salinas. ConclusionsThe application of selected yeast to cachaca production can contribute for the improvement of the quality product as well as be used as a natural marker for PDO. Significance and Impact of the StudyThis study suggests that the use of selected yeast strains could contribute to obtain a cachaca similar to those produced traditionally, while getting wide acceptation in the market, yet presenting more homogeneous organoleptic characteristics, and thus contributing to the PDO implementation.