Yeast has played an important role in human cultures since their ancient domestication, and their biochemical versatility, tolerance of different stress factors, and the ease of traditional and later molecular strain improvement strategies have only increased their roles in many agricultural and industrial fields. During industrial processes e.g., fermentation, yeast experiences multiple stress factors, and it shows adaption to the changing environment by exhibiting clonal heterogeneity, which underlines genome structure variations(GSV). In this thesis, I hypothesized that clonal heterogeneity may already have considerable effects on the heritable phenotypes of industrial yeast: subclone lineages may already be diverse and inherently heterogeneous inside products. I obtained bioethanol, wine, beer/ale, lager, probiotic, and bread yeasts from the various manufacturers, and I found how heterogeneous these yeasts are when industrially important stress phenotypes are considered. I measured the frequency of colony phenotype switches and petite mutations (yeasts with defunct mitochondria). Moreover, due to the diversity in the genetic makeup, the clonal lineages that have accumulated heterogeneity exhibited diverse responses to stress factors and different sub-clones (emerged as a result of clonal heterogeneity and clonal interference) showed high-stress tolerance and elevated population fitness. Thus, it may be advantageous for industries to consider these stochastic processes for strain improvements and predictable yield.