Carbohydrate degrading enzymes produced by fungus such as Aspergillus are interesting due to its application into process of ethanol production using cheap materials such as agro-wastes. Proteins of xylanolytic system which are secreted during Aspergillus flavipes FP-500 culture with corn cobs as a carbon source, are adsorbed in the solid matrix of cobs unlike wheat bran in which virtually are non-absorbed. Recovery of proteins with washing solutions from both agro-wastes and protein sequences of some of these proteins shows: that increase of pH improves protein desorption, adsorption of xylanolytic system proteins is pretty much selective in wheat bran than in corn cobs and the adsorption of that proteins could be influenced by random interaction between protein and polysaccharide surface as well as specific interactions of proteins with polysaccharides by carbohydrate binding domains of certain involved proteins.