Genotoxicity of crude cyanobacteria extracts (CBE) from blooms in Taihu Lake, China toward common carp (Cyprinus carpio) was measured. The primary extracellular product was determined by HPLC to be Microcystin-LR (MC-LR, L for leucine and R for arginine) with an average concentration of 2.4 × 102 μg MC g−1 dry weight of cyanobacteria. Acute toxicity to carp, expressed as the 72-h LC50, was 53 mg, dw cyanobacteria L−1. Genotoxicity, as determined by the micronucleus (MN) and comet assays were both dose- and time-depended. Deformities of cellular organelles in liver and gill were observed by use of transmission electron microscopy (TEM). The results showed that MC-LR from cyanobacteria from Taihu Lake could induce genotoxic response and tissue-level morphological changes in common carp.