Members of the Saccharomyces genus have played a key role in genetic research and are widely utilized in industrial applications. However, much is sill unknown about their wild population structure, genetic diversity, and domestication for fermentation applications. One species in this genus, Saccharomyces eubayanus, is a parent of the hybrid lager yeasts and, despite its important role in brewing, in the wild, it has never been isolated in Europe and is mainly isolated in Asia and South America. S. eubayanus’ role in industry and its global distribution allows us to ask evolutionary questions of domestication and wild population structure across different time scales from ancient to modern. Utilizing whole genome sequencing data and population genomic techniques, we have begun to disentangle S. eubayanus’ current demographics and elucidate the genetic diversity at the time of hybridization to form lager yeasts. Analysis of all genomes currently available shows two major populations of S. eubayanus; with evidence of an ancient population split, followed by subsequent secondary contact and gene flow primarily into only one of the populations. Within one of the major populations there are several subpopulations whose genetic diversity and geography inform our understanding of its complex past and present demography. One subpopulation has only been found in the Holarctic ecozone and includes the lager lineages. From this subpopulation, we can infer the diversity of the ancient subpopulation that gave rise to lager yeasts despite having few modern representatives of this subpopulation. Another subpopulation contains closely related strains largely from Patagonia, but also Oceania and North America suggesting the potential for migration and niche expansion. Finally, adding to our understanding of recent population dynamics is enhanced by a lineage that is the result very recent admixture of the two the major populations. Interestingly this lineage is found in two locations in North America, suggesting that this admixed group can thrive outside of Patagonia and raising questions of the migratory possibilities of this yeast. S. eubayanus’ dynamic population structure has allowed us survey ancient to modern gene flow and work back in time to illuminate our knowledge of the subpopulation that gave rise to lager yeasts. Understating the modern population structure and diversity of industrially important yeasts informs our understating of both the wild dynamics of yeasts and the different paths taken to domesticate this important genus.