A novel mathematical model of aerated shaking bioreactors is developed and its accuracy is evaluated with experimental data. Corynebacterium glutamicum (DM 1730) and Arxula adeninivorans (WT LS3) are used as model microorganisms. In order to get the experimental data, shake flasks of 250 mL and filling volume of 15 mL, together with online measurement tools for measuring oxygen transfer rate and tools for measuring dry biomass concentration, are used. This mathematical model may be regarded as a key tool for computational simulations or developing model-based control approaches for necessary automation and optimization purposes. Moreover, the error evaluation presented in this paper should be taken into account when using the model. The squared Pearson product-moment correlation coefficient (r2) and average deviation of error are used as two statistical criteria to quantify the accuracy and consistency of the model. The r2 for biomass concentration equals 0.95 for C. glutamicum (DM 1730) and 0.93 for A. adeninivorans (WT LS3). The reported average deviation of error of biomass concentration approaches 17.4% for C. glutamicum (DM 1730) and 26.7% for A. adeninivorans (WT LS3).