Micronucleus test is conducted by using Vtcia faba root tips to detect the mutagen pollution in Taihu Lake. The results show that some water areas of the lake have been slightly polluted by mutagens. The pollution areas are Wuli Bay and some river mouth areas along northwest bank or coast. The pollution level is varied with the water level of the lake. During the lower water level stage the pollution is more serious than that in higher water-level stage. Also the pollution areas will change with the water level flunctuation. In Liangxi River mouth area, the pollution during higher water level stage is slighter than that during lower water level stage as the water inters from lake into the Liangxi River where the water is polluted seriously by the domestic wastewater of Wuxi City. Correlative annlyzation between water quality parameters and micronucleus index show that micronucleus index is closely related with physio-chemical parameters to assess water quality. Some measurements are proposed for the conservation and pollution control of Taihu Lake.