Computational fluid dynamics simulation is becoming an increasingly useful tool in the analysis and design of simultaneous saccharification fermentation (SSF) and saccharification followed by fermentation process (SFF). To understand and improve mixing and mass transfer in a highly viscous non-Newtonian system, it was necessary to simulate the flow behavior in this bench scale bioreactor (BioFlo 3000). This study focused on designing a high concentration medium agitation system for such a process using the commercial computational fluid dynamics package Fluent (V. 6.2.20) and its preprocessor Mixsim (V. 2.1.10). The objective of this study is to ompare performance of various designs of a bioreactor and identify the flow pattern and related phenomena in the bench scale tank. The configuration of the physical model for simulating a mixing tank with a Rushton impeller consists of an ellipsoidal cylindrical tank with four equally spaced wall mounted baffles extending the vessel bottom to the free surface, stirred by a centrally located six-blade Rushton turbine impeller. Simulations were performed with the original and a modified design in which the lower bottom shaft mounted a Lightnin A200 impeller. The results suggest that there is a potential for slow or stagnant flow between top impellers and bottom of the tank region, which could result in poor nitrogen and heat transfer for highly viscous fermentations. The results also show that the axial velocity was significantly improved for the modified geometry in the bottom of the tank.