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The product formation of the biopellets of filamentous fungi, such as Aspergillus niger, is closely linked with the pellet morphology. Therefore, investigations were carried out to determine the influence of fluid dynamic conditions on the growth of fungal pellets. During the present study, important information about the evolution of morphological changes during the cultivation process in stirred tank reactors was gathered from cultivations at different volumetric power inputs by agitation and aeration. The quantification of the pellet morphology was accomplished by the digital image analysis and the laser diffraction technique tracing parameters like the pellet diameter and the pellet concentration. The property of the pellet surface structure was determined by the microscopic image analysis of the pellet slices and verified by sedimentation velocity measurements. Results revealed a notable variation in morphological data among pellets cultivated at different volumetric power inputs by agitation and aeration, by which the production yields of the model product glucoamylase were correspondingly altered. Furthermore, without raising the total energy input, by utilizing of the different impact of aeration- and agitation-induced volumetric power input on the fungal pellet morphology, the product formation could be consequentially improved.