At present, the genus Saccharomyces comprises seven species according to their patterns of breeding. The species boundaries are not clear due to the description of several reticulate events due to introgression and hybridization. In the last decade, new natural hybrids have been described in wine and brewing, such as S. cerevisiae x S. kudriavzevii. Due to new practices in wine and beer production, together with consequences in grape properties due to climatic change, led biotechnological companies to search for new yeast strains. In this context, hybrids have become of importance to biotechnological industries because they show good fermentative performance at low temperatures and produce new organoleptic compounds of industrial interest. This doctoral thesis explores the evolution of the natural S. cerevisiae x S. kudriavzevii hybrids and the importance of hybridization in the evolution of the Saccharomyces species. This study was performed by using different molecular approaches combined with bioinformatic tools for phylogenetic tree/networks reconstruction and data analysis. Understanding the origin and genome characteristics of natural S. cerevisiae x S. kudriavzevii hybrids are our priority for obtaining, in the future, personalized yeasts with new properties of biotechnological interest.