Kazachstania aerobiaandKazachstania servazziican affect wine aroma by increasing acetate ester concentrations, most remarkably phenylethyl acetate and isoamyl acetate. The genetic basis of this is unknown, there being little to no sequence data available on the genome architecture. We report for the first time the near-complete genome sequence of the two species using long-read (PacBio) sequencing (K. aerobia20 contigs, one scaffold; andK. servazzii22 contigs, one scaffold). The annotated genomes ofK. aerobia(12.5 Mb) andK. servazzii(12.3 Mb) were compared toSaccharomyces cerevisiaegenomes (laboratory strain S288C and wine strain EC1118). Whilst a comparison of the twoKazachstaniaspp. genomes revealed few differences between them, divergence was evident in relation to the genes involved in ester biosynthesis, for which gene duplications or absences were apparent. The annotations of these genomes are valuable resources for future research into the evolutionary biology ofKazachstaniaand other yeast species (comparative genomics) as well as understanding the metabolic processes associated with alcoholic fermentation and the production of secondary ‘aromatic’ metabolites (transcriptomics, proteomics and metabolomics).