Mathematical modeling of hydantoinase production system from microbial sources, which would help to understand the mechanism of the process, has not been attempted earlier. This paper tries to model five state variables (biomass, substrate, product (D-hydantoinase), Oxygen Uptake Rate (OUR) and carbon dioxide production rate (CPR)) for three carbon sources namely glucose, glycerol and maltose in the production of D-hydantoinase using Agrobacterium radiobacter as source. Several models were tested to fit the aerobic batch experimental data from a 3 L bioreactor. The best fitting model consisted of (a) biomass growth non-linearly dependent on substrate concentration, (b) product formation rate following exponential form of product inhibition and (c) OUR following positive regulation by substrate. D-hydantoinase production in maltose experiences minimal lag phase and stronger product inhibition when compared to glycerol. Maltose showed higher biomass yield (0.25) and specific D-hydantoinase production (27.44 U mg-1) compared to glycerol whose values are 0.18 and 21.97 U mg-1, respectively.