A mathematical model describing intracellular lysine synthesis by Corynebacterium glutamicum in batch fermentation was developed. The model is based on material balance equations of the key metabolites, and includes mechanistically based, experimentally matched rate equations for individual enzymes. From the measurements of the levels of intra- and extracellular metabolites during cultivation, the kinetic parameters in the model were identified through the decomposition of the network of reactions. The model predictions and experimental observations were in reasonable agreement. Using the model developed, metabolic control analysts was carried out to identify the rate-limiting steps, by evaluating the control on the overall lysine synthesis flux exerted by individual enzymatic reactions, which suggested how the control on lysine synthesis changes from aspartokinase to lysine permease as fermentation proceeded and indicated that lysine production could be enhanced by improving aspartokinase activity of this strain through genetic manipulation.