In the last several years the relationships among the strains previously referred to as Saccharomyces bayanus, have been clarified. This has led to the splitting of these strains into the sister species Saccharomyces uvarum (formerly S. bayanus var. uvarum) and Saccharomyces eubayanus (previously the unknown S. bayanus-like contributor to hybrid lager yeasts), and a complex of multi-species hybrids. Hybrids of S. eubayanus and S. uvarum display more than 10x the spore viability of any other Saccharomyces hybrid pair, greatly facilitating genetic studies. Intriguingly, while these species are roughly 10% diverged at the nucleotide level, they are sympatric in nature and, apparently, very physiologically similar. Despite this however, brewing strains of each species (always Saccharomyces cerevisiae hybrids or introgressed strains) are strongly allied with different types of fermentations: wines and ciders for S. uvarum and lager style beers for S. eubayanus. To better understand what separates these industrially important yeasts we have begun exploring the phenotypic and genetic diversity within and between S. eubayanus and S. uvarum. By comparing the whole-genome sequences of hybrid lager yeasts with their parent species we found that the S. eubayanus portion of the lager yeast genomes has experienced pronounced and pervasive relaxation of selective pressure. In addition, we also identified several gene clusters that are likely to be important for S. eubayanus’ contribution to maltose consumption, which is essential for efficient fermentation. With gene knockout and replacement studies we are further exploring this essential industrial trait. To determine the genetic and phenotypic basis of separation between S. uvarum and S. eubayanus, both in nature and in human related fermentations, we are using genome comparisons and analysis of hybrids. Preliminary studies of hybrids indicate possible difference in RNA metabolism, potentially providing insight into the functions of RNA metabolism in ancestral Saccharomyces and extant yeast lineages. By studying the diversity contained both within and between these species we not only increase our understanding of this pair of industrially important yeasts, but as an early branching lineage of the Saccharomyces they can shed light on the evolution of some peculiar traits, such as the early loss of RNAi, in this important model genus.