Ethanol toxicity is a major challenge forS. cerevisiaeduring fermentation, affecting its growth and influencing the process. This study investigated the molecular mechanisms of ethanol tolerance using transcriptomic analysis of threeS. cerevisiaestrains with varying ethanol resistance. We identified distinct responses in membrane lipid synthesis genes, particularly in ergosterol biosynthesis, regulated by the Ino2p transcription factor. A variant of Ino2p with V263I and H86R amino acid replacements was exclusive to ethanol-tolerant strains. CRISPR-Cas9-mediated point mutations in theINO2gene of the highly tolerant strain AJ4 resulted in decreased ethanol tolerance. Our findings demonstrate the crucial role of Ino2p in ethanol tolerance through regulation of lipid synthesis and membrane composition, highlighting the complex interplay of trans elements in strain-specific ethanol resistance.