The kinetics of Se(VI) reduction by a defined co-culture of a Se(VI)-reducing strain Shigella fergusonii TB42616 (TB) and a Se(IV)-reducing strain Pantoea vagans EWB32213-2 (EWB) was investigated in batch reactors. Se(VI) reduction was a two-stage process from Se(VI) to Se(IV) and then from Se(IV) to Se(0). Biokinetic parameters were optimized with a Monod-type kinetic model using batch pure culture data through the Robust Global Optimization Algorithm embedded in a computer package including yield coefficients, decay coefficients, maximum specific growth rates, and half-velocity constants. Se(VI) reduction by the defined co-culture was then simulated and verified over a range of culture compositions and initial Se(VI) concentrations, respectively. An inter-species inhibition term was incorporated into the model to illustrate the competition for Se(IV) between these two species during Se(VI) reduction in the co-culture. The results indicated that the incubation time corresponding to the peak level of Se(IV) increased with initial Se(VI) concentrations and a significant increase of Se(IV) accumulation with higher initial Se(VI) concentration. However, Se(IV) accumulation can be reduced with increasing population ratio of EWB to TB. The relatively high correlation coefficients suggested that the model was robust and applicable in simulating Se(VI) reduction by the defined co-culture.