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In this study a membrane bioreactor (MBR) using white-rot fungi was used for the decolorization of dye solutions. The decolorization of dye solutions by Trametes versicolor KCTC 16781 and membrane filtration were combined, and the applicability of this process was investigated using reactive dye solutions. The feasibility of MBR using fungal biodegradation was studied with nanofiltration and reverse osmosis (RO) membranes to improve permeate flux and separation efficiencies. The effects of dye types on fungal biodegradation and membrane filtration (permeate flux and rejection) were also investigated. The fungal MBR combined with RO was found effective for decolorization and organic removal of dye wastewater.