<p>Species evolution has long been associated exclusively with vertical gene transfer, making genetic variability a result of recombination and spontaneous mutations. Although long considered exclusive to prokaryotes, horizontal gene transfer (HGT), plays an important evolutionary role even in complex eukaryotic lineages. This process can generate novel functions in the host, proving evolutionary paths not predicted by vertical inheritance. This review highlights how HGT has significantly shaped the genome evolution of <i>Saccharomyces cerevisiae</i>, providing key traits relevant to fermentation processes. HGT events from bacteria, alongside introgression from other yeasts, contribute to the genetic diversity and specific adaptations seen in domesticated strains of <i>S. cerevisiae</i>, distinguishing them from wild relatives and influencing their industrial utility. Here we report how the advent of next-generation sequencing (NGS), and the subsequent flood of genomic data, have fundamentally accelerated the discovery and analysis of HGT events across all domains of life. The sheer volume of NGS data has driven the development of sophisticated bioinformatics tools and algorithms specifically designed to detect the phylogenetic and compositional signatures of HGT. We also discuss how detecting HGT events helps to understand yeast genome plasticity and to identify useful “foreign” DNA, which can then be manipulated to create novel yeast strains with enhanced fermentation performance, flavour profiles, or stress tolerance.</p>