Biomarkers in higher plants played an important role to estimate exposure effects of pollutants in soil ecosystem and have received increasing attention in recent years. The qualitative and quantitative modifications arising in amplified fragment length polymorphism (AFLP) profiles as a measure of DNA effects were compared with a number of parameters, namely, the root length,total soluble protein content in root tips, chlorophylls content and shoot size to select the most sensitive biomarker responding to copper stress in the range of 0-600 mg/kg. The changes occurring in AFLP profiles of root tips following Cu treatment included loss of normal bands and appearance of new bands and variation in band intensity in comparison to that of the normal seedlings. A reduction in root length was observed at the 200 mg/kg of copper, which was accompanied with a decrease in total soluble protein content. According to their sensitivity to the copper toxicity, the above indicator rank in the following order: AFLP profiles＞total soluble protein content＞root length＞chlorophylls content＞shoot. We concluded that the AFLP offered a useful alternative biomarker assay for the detection of genotoxic effects of environmental pollutants.