The AFLP analysis was carried out in order to evaluate the DNA damaging effects of dyestuff of different concentrations on Phanerochaete chrysosporium. The DNA similarity and UPGMA cluster analysis were conducted to determine the relationships between the concentrations of dyestuff and DNA damaging effects. The results showed that the AFLP analysis could reflect the polymorphisms of DNA well, and the primer pairs E-AAC/M-CAA could give more amplified DNA fragments than others primers. From the DNA maps of best primer pairs, 35 clear and stable DNA bands were observed, including 12 polymorphous bands which were accounted for 34.3% diversity. It was indicated from the DNA similarity and UPGMA cluster analysis that DNA polymorphisms correlated with dyestuffs concentrations well. If the concentration of dyestuff was not higher than 50 mg/L, the damaging effect on DNA was finite. If the concentrations of dyestuff were up to 300 mg/L, the DNA of Phanerochaete chrysosporium would have been injured greatly, and would have been bankrupted in its intrinsic function.