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We report the first complete circular genome of Acetobacter cerevisiae KSO5, an indigenous strain isolated from Korean fruit vinegar, comprising a 3.3 Mb chromosome and two plasmids encoding 2,898 genes. Phylogenomics confirmed species assignment (average nucleotide identity, ANI 97%; digital DNA–DNA hybridization, dDDH 71%). Comparison with seven draft A. cerevisiae genomes revealed strain-specific genomic islands, mobile genetic elements and polymorphisms in stress-response pathways, with enrichment in acid-tolerance–associated functions, and highlighted plasmid-borne modules potentially linked to genetic stability. The genome encodes a periplasmic oxidative fermentation system with membrane-bound pyrroloquinoline quinone-dependent alcohol dehydrogenase (PQQ-ADH) and molybdopterin-dependent aldehyde dehydrogenase (Mo-ALDH), together with respiratory-chain components consistent with flexible aerobic metabolism. Three acetate-handling routes (efflux, acetyl-CoA conversion and an AarC branch) were also predicted, suggesting mechanisms to limit intracellular acetate accumulation. Consistent with these features, phenotyping under ethanol stress (5–10%) showed measurable growth and titratable acidity production up to 9% ethanol (late-stage peak acidity). These data provide a genomic and phenotypic basis for developing robust vinegar starter cultures.