Mezcal is an alcoholic beverage obtained by distilling musts and juices fermented by spontaneous or cultivated microorganisms, which are extracted from ripe stems of cooked Agaves and harvested in Mexico. Both raw material and production practices differ markedly between producing regions, locations, and even factories, resulting in a very distinctive set of products. The state of Oaxaca is the top producer worldwide of mezcal, and 35,000 families are involved in the production of this aromatic alcoholic beverage. Fermentation is the most important stage of mezcal production and is performed by different yeast and bacteria. In this study, the yeast strains were isolated from fermentation containers of four mezcal factories (palenques) in Oaxaca. Taxonomic determination was verified by ITS, and an analysis of the biotechnological process through personal interviews and principal component analysis was performed. Eighteen different isolates of eight different genera (Candida, Clavispora, Meyerozyma, Metarhizium, Pichia, Saccharomyces, Torulaspora, and Yarrowia) were identified. According to the biotechnological process analysis and principal component analysis, the artisanal palenques (palenques 1, 3, and 4) are more like each other than and differ radically from palenque 2, which is where the artisanal process has changed towards technical production.