The acute and sub-chronic toxicities of cyanobacterial extract from Taihu Lake (PR China) on mouse (Mus musculus) were investigated in this study via intraperitoneal (i.p.) injection. Increases in liver/body weight ratios and pathological changes in mouse liver showed adverse effects at the organ level. Images from transmission electron microscopy (TEM) indicated that abnormal membrane structure occurred and that the organelles were damaged severely in the cells of liver and testis. The high dose group received i.p. injection of 12 mg lyophilized algae cells/kg body weight. Malondialdehyde (MDA) levels increased significantly in the livers of this group, along with a significant decrease in catalase (CAT) activity. These results revealed the existence of obvious oxidative stress. Comet assay results also suggested a dose-dependent relationship between DNA damage in hepatocytes/testicular cells and the amount of bloom extract administered to the mice. There was a significant increase in DNA damage compared to the control group and the genotoxicity of the cyanobacterial bloom to testicular cells was higher than in hepatocytes.