To further elucidate the biosynthesis of lipids in flor strains under fermentative conditions, the transcription levels of the lipid biosynthetic genes ACS1, ACS2, ACC1, OLE1, ERG1, ERG11, ARE1 and ARE2, as well as the lipid composition and cell viability of a flor strain were compared with that of a non-flor strain during hypoxic and aerobic fermentations in the absence of lipid nutrients. While no significant differences in transcription levels or lipid compositions were observed between the two strains when oxygen was not limiting, significant differences were seen during hypoxic fermentation. In this last condition, the flor strain, in spite of higher levels of transcription of hypoxic genes, lost the abilities to desaturate fatty acids and complete ergosterol biosynthesis, and showed a dramatic loss of viability. In contrast, the non-flor strain, which showed lower transcription levels, was able to reach a balanced lipid composition and maintained a higher cell viability. One possible explanation is that the flor strain requires a higher amount of oxygen than the non-flor strain in order to carry out the oxygen-dependent steps of lipid biosynthesis under fermentative conditions.