Deep tank fermentations are widely used in the production of enzymes, antibiotics and organic acids, which have many applications in the food, medicine, pharmaceutical, chemical and textile industry (Mitard and Riba, 1987). The diverse range of commercially exploited fungal products, which have large contribution to the global economy is expanding enormously. However, their filamentous growth characteristic creates a number of process engineering problems attributed to the morphological change accounted during the fermentation process in large scales. This effects the maximum product and productivity of an enzyme. In this study, pectinase enyzme production was taken as a model for submerged fermentation. For this purpose, Aspergillus sojae strain which is not well known in the literature, was taken as a model organism and subjected to fermentation at 30 o C for 96 hours to produce pectinase enzyme of commercial value. Composition of media, inoculation ratio and type, temperature and aeration rate was kept constant during fermentation. Experiments were conducted according to different dissolved oxygen concentrations, agitation speeds and pH in order to investigate the effects of these parameters on rheology, morphology and activity. As a result of these experiments, it was observed that small pellets gave higher activities under the conditions of low agitation speed, high dissolved oxygen concentrations and uncontrolled pH.