W303 is a laboratory strain of Saccharomyces cerevisiae that has been employed to study a multitude of biological processes. Many of these studies require a reference quality genome sequence for single nucleotide polymorphism identification and other high-throughput or hybridization-based molecular analyses. In this work, we present a high quality genome sequence that can be utilized for genome-wide studies. Comparative analysis with an ancestor of W303, S288c, provides insights into the evolutionary past of this laboratory strain. About 91 % of the genome sequence of W303 is identical to S288c; however, several divergent gene families have been analyzed. Selective pressures acting on flocculation genes were characterized, these represent selection against invasive strains. Remnants of ancestor wine strains have been identified on several chromosomes.