This study presents a comprehensive population genomics analysis of *Saccharomyces cerevisiae* and its closest relative, *S. paradoxus*. The researchers sequenced over seventy isolates of both species to one to four-fold coverage, examining gene content, SNPs, indels, copy numbers, and transposable elements. They found that phenotypic variation correlates with global genome-wide phylogenetic relationships. *S. paradoxus* populations are well-delineated along geographic boundaries, while *S. cerevisiae* isolates show less differentiation, comparable to a single *S. paradoxus* population. The population structure of *S. cerevisiae* consists of a few well-defined geographically isolated lineages and many mosaics of these lineages, suggesting that human influence facilitated cross-breeding and the production of new combinations of pre-existing variation. The study also highlights the complex population structure of *S. cerevisiae*, with five well-delineated lineages and many recombinant strains. Phenotypic analysis revealed a high qualitative overlap between genotypic and phenotypic clustering, indicating that the higher phenotypic variance in *S. cerevisiae* is not driven by outbreeding or domestication but rather by its broader ecological niche. The findings provide insights into the evolutionary processes acting within populations and species, contributing to our understanding of genome evolution and the adaptation to different environments.This study presents a comprehensive population genomics analysis of *Saccharomyces cerevisiae* and its closest relative, *S. paradoxus*. The researchers sequenced over seventy isolates of both species to one to four-fold coverage, examining gene content, SNPs, indels, copy numbers, and transposable elements. They found that phenotypic variation correlates with global genome-wide phylogenetic relationships. *S. paradoxus* populations are well-delineated along geographic boundaries, while *S. cerevisiae* isolates show less differentiation, comparable to a single *S. paradoxus* population. The population structure of *S. cerevisiae* consists of a few well-defined geographically isolated lineages and many mosaics of these lineages, suggesting that human influence facilitated cross-breeding and the production of new combinations of pre-existing variation. The study also highlights the complex population structure of *S. cerevisiae*, with five well-delineated lineages and many recombinant strains. Phenotypic analysis revealed a high qualitative overlap between genotypic and phenotypic clustering, indicating that the higher phenotypic variance in *S. cerevisiae* is not driven by outbreeding or domestication but rather by its broader ecological niche. The findings provide insights into the evolutionary processes acting within populations and species, contributing to our understanding of genome evolution and the adaptation to different environments.