Large quantities of deeply pigmented molasses distillery wastewater (MDW), are discharged during the production of bio-ethanol from molasses. Conventional biological wastewater treatment is not effective in removing the molasses pigments. In the present study, a MDW treatment system was developed with combination treatment involving biodecolorization and biotreatment by Aspergillus tubingensis DCT6, together with physical decolorization by ozonation after treatment by activated sludge. A. tubingensis DCT6, which was isolated from soil, decolorized 44% of the pigments in MDW without adding any nutrients. The combination treatment with A. tubingensis DCT6 and activated sludge method (fungi-activated sludge treatment) removed about 90% of organic compounds from MDW and appears to reduce the amount of space and water required for treatment. The fungi-activated sludge treatment reduced the time needed for decolorization by ozone by 83%. Replacing fresh seed sludge at regular intervals was useful to maintain the dominance and decolorization ability of A. tubingensis DCT6. The entire treatment obtained a decolorization ratio of 89–94% and removed more than 90% of each of DOC, DTN, and DTP.