Mezcal is a spirit produced in some regions of México. In the state of Durango, mezcal is produced via traditional fermentation of the Agave duranguensis plant. To better understand traditional fermentation processes, it is necessary to know which yeast species are present in fermentations in different producer regions. The aim of this research was to study yeasts involved in traditional mezcal fermentation in Durango, México, and investigate the phylogeny of the native Saccharomyces cerevisiae strains involved in this process. The 5.8S-ITS genomic region was analyzed to identify strains present in the fermentation process samples in this study. To differentiate strains belonging to the genus Saccharomyces, different molecular techniques were used, including analysis of mitochondrial DNA and δ elements and sequencing of the 5.8S-ITS genomic region. Although a high diversity of microorganisms was found at the beginning of fermentation, Saccharomyces cerevisiae was the only yeast present at the end of fermentation in region I, while Torulaspora delbrueckii was found in a higher number than S. cerevisiae at the end of fermentation in the region II. Molecular techniques demonstrated that Saccharomyces cerevisiae isolated in Durango are phylogenetically independent from the strains isolated in other regions of Latin America and Europe.