Temperature is arguably the leading factor that drives adaptation of organisms and ecosystems. Remarkably, many sister species share the same habitat because of their different temporal or micro-spatial thermal adaptation. In this PhD, the underlying molecular mechanisms of the adaptation of closely related species to different temperatures are sought. A thermodynamic analysis was applied to a genome-scale metabolic model of S. cerevisiae at warm and cold temperatures to identify thermo-dependent reactions. Gene Ontology (GO) analysis of predicted cold-dependent reactions found that redox reactions were significantly enriched. A complementary large scale experimental approach was taken by competing 6,000 mutant strains at 16°C to identify genes that were responsible for the fitness at low temperatures. The experiment was carried out in three different nutritional conditions to test the plasticity of temperature dependency. A list of strains whose copy number significantly increased or decreased in all media conditions was constructed and analysed using Gene Ontology. Vitamin biosynthesis, lipid/fatty acid processes and oxido-reduction reactions were all found to be significantly affected by the cold condition. Combining the data from the two studies a list of candidate genes affected by temperature changes were generated. In particular, two genes, GUT2 and ADH3, were identified as potential cold favouring genes and studied in more detailed. Mutants for these two genes were created in a pair of natural sympatric cryotolerant and thermotolerant Saccharomyces yeasts, namely S. kudriavzevii CA111 and S. cerevisiae 96.2, representing an excellent ecological experimental model for differential temperature adaption. My results showed that when compared to the parental strains, both mutants showed lower fitness at cold temperatures as predicted, and in S. kudriavzevii CA111 these mutations significantly improve growth at warm temperatures. Results from all aspects of this work indicate that oxidation reduction reactions are important for cold acclimation. It is known that heat stress causes redox imbalances which are compensated by increasing glycerol production or cytosolic acetaldehyde. Since GUT2 and ADH3 are involved in these processes, mutations in these genes may not be able to compensate for temperature changes. My data also shows that vitamins may also play an important role in cold acclimation which would be an interesting line of investigation for future work. Overall this PhD thesis has incorporated in silico and in vivo work to identify potential processes and genes involved in the temperature adaptation of sister Saccharomyces yeast species. The approach and results provided in this study support the use of a systems biology framework to studying species adaptation to environmental changes, and show that such models can yield testable predictions that may lead to new biological discoveries.