Genome sequences of multiple individuals are essential to determine the forces shaping sequence variation as well as to understand the relationship between genotype and phenotype. Because of their wide ecological, geographical and genetic diversity, yeast species represent an ideal model system for population genomics. Recently, we were interested in characterizing the genetic diversity within yeast species such as Saccharomyces cerevisiae and Saccharomyces kluyveri. We are currently exploring the intraspecific diversity using large collections of yeast isolates of different species. These large-scale polymorphism surveys increase our understanding of the population structures as well as the evolutionary history of the species. In addition, these resources represent a powerful framework for dissecting the relationship between genotype and phenotype.