Acid-producing fungi can be used for the treatment of black liquor by biological acidification for the precipitation of alkali lignin. The effects of alkali lignin obtained from black liquor on the growth, acid-producing capacity and glucose consumption of a brown-rot fungus Fomitopsis sp. IMER2 were investigated and the changes in the functional group in the resulting alkali lignin were analyzed by Fourier transform infrared (FTIR) spectroscopy. Although the presence of alkali lignin inhibited fungal growth and acid production, it enhanced glucose consumption. This suggests that the physiological response of this fungus to stress induced by alkali lignin is unique. Furthermore, the analysis of the effects of the resulting alkali lignin on the growth rate showed that several functional groups were evidently improved for the use of available resources.