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The internal transcribed spacer (ITS) region was used to discriminate 18 Saccharomyces cerevisiae strains isolated from fermented foods of the North-Western Himalayas. ITS sequences were compared with other known lineages available in literature. A phylogenetic tree grouped these strains into two clusters, the first comprising Malaysian, North American, Sake, West African and wine/European strains and the second comprising all Indian strains along with certain other strains from different countries. In both clusters, mixed grouping was observed, with the exception of a few strains with a region-based grouping pattern. The baking and brewing abilities of these strains were studied to expose functional diversity. Four strains, viz. Sc06, Sc11, Sc19 and Sc20, were found promising for baking and three strains, viz. Sc04, Sc05 and Sc24, were found promising for brewing, thereby indicating the existence of functional diversity. At a genetic level, mining of the ADH1 gene of ten randomly selected yeast strains, showed very little variation in the gene sequences irrespective of their alcohol production ability. In contrast, mining of the ATF1 gene showed a lot more variation in the gene sequences, revealing the ATF1 gene to be an appropriate marker to reveal differences in ester formation among these indigenous yeast strains.