Cyanobacterial bloom promotes pollution of the eutrophic lakes and affects the stability of lake ecosystems. In the present research we detected DNA damages and micronucleus blood cells of Procambarus clarkii in Lake Caizi and Lake Chaohu, two different eutrophic lakes along the Yangtze River in Anhui Province by micronucleus test and comet assay to assess the genetic toxicity effects on the blood cells during the period from April to September, 2010. The lowest micronucleus ratios were 0.316±0.131 and 0.243±0.063, and the highest values were 0.624±0.136 and 0.360±0.081 in Lake Chaohu and Lake Caizi, respectively. The highest values of the three indicators of DNA damage ratios, TailDNA, TM and OTM, which occurred in Lake Chaohu, were 7.59±1.58, 2.75±1.55, 3.12±1.45, respectively, and 5.02±1.42, 1.07±0.16, 1.19±0.26, respectively in Lake Caizi. DNA damage and micronucleus ratios increased with time in the two lakes, and in Lake Chaohu during the period from June to July by large amplitude. The DNA damage and micronucleus reached significant differences between the two lakes in July, August and September. Detection results were the same for the two different tests, but comet assay was more sensitive then micronucleus test. So we suggest that it's necessary to combine the two tests to get more effective detection of genetic toxicity.