ABSTRACT Spathaspora passalidarum NN245 (NRRL‐Y27907) is an ascomycetous yeast that displays a higher specific fermentation rate with xylose than with glucose. Previous studies have shown that its capacity for xylose fermentation increases while cell yield decreases with decreasing aeration. Aeration optimization plays a crucial role in maximizing bioethanol production from lignocellulosic hydrolysates. Here, we compared the kinetics of S. passalidarum NN245 and Scheffersomyces (Pichia) stipitis NRRL Y‐7124 fermenting 15% glucose, 15% xylose, or 12% xylose plus 3% glucose under four different aeration conditions. The maximum specific fermentation rate for S. passalidarum was 0.153 g ethanol/g CDW · h with a yield of 0.448 g/g from 150 g/L xylose at an oxygen transfer rate of 2.47 mmol O2/L h. Increasing the OTR to 4.27 mmol O2/L h. decreased the ethanol yield from 0.46 to 0.42 g/g xylose while increasing volumetric ethanol productivity from 0.52 to 0.8 g/L h. Both yeasts had lower cells yields and higher ethanol yields when growing on xylose than when growing on glucose. Acetic acid accretions of both strains correlated positively with increasing aeration. S. passalidarum secreted lower amounts of polyols compared to S. stipitis under most circumstances. In addition, the composition of polyols differed: S. passalidarum accumulated mostly xylitol and R,R‐2,3‐butanediol (BD) whereas S. stipitis accumulated mostly xylitol and ribitol when cultivated in xylose or a mixture of 12% xylose and 3% glucose. R,R‐2,3‐BD accumulation by S. passalidarum during xylose fermentation can be as much as four times of that by S. stipitis, and R,R‐2,3‐BD is also the most abundant byproduct after xylitol. The ratios of polyols accumulated by the two species under different aeration conditions and the implications of these observations for strain and process engineering are discussed. Biotechnol. Bioeng. 2015;112: 457–469. © 2014 Wiley Periodicals, Inc. Spathaspora passalidarum fermented xylose more efficiently than glucose under micro‐aerobic conditions. The maximum ethanol yield was 0.46 g per g xylose consumed or 90% of maximum theoretical. Maximum volumetric productivity was 0.8 g/L h. R,R‐2,3‐butanediol was the second highest product formed by S. passalidarum. Fermentation rates and yields were higher than those of Scheffersomyces stipitis when cultivated under the same conditions, implying that the glycolytic flux of S. passalidarum is higher than that of S. stipitis.