D-Ribose is a value-added five-carbon sugar used for riboflavin production. To investigate the effects of oxygen supply and mixed sugar concentration on microbial production of D-ribose, a transketolase-deficient Bacillus subtilis SPK1 was cultured batch-wise using xylose and glucose. A change of agitation speed from 300 rpm to 600 rpm at 1 vvm of air supply increased both the xylose consumption rate and D-ribose production rate. Because the sum of the specific consumption rates for xylose and glucose was similar at all agitation speeds, metabolic preferences between xylose and glucose might depend on oxygen supply. Although B. subtilis SPK1 can take up xylose and glucose by the active transport mechanism, a high initial concentration of xylose and glucose was not beneficial for high D-ribose production.