Microcystin-LR (MC-LR) is one of the hepatotoxins produced by cyanobacteria in the eutrophicated fresh water. In this work, the minor groove binding mode of MC-LR to plasmid DNA was explored by using UV and fluorescence spectra, and the binding characteristics of MC-LR for plasmid DNA were calculated via the fluorescence quenching of ethidium bromide (EB) and mole ratio method. Furthermore, atomic force microscopy (AFM) was used to observe DNA morphology change in the presence of MC-LR. With the increasing concentration of, MC-LR, circle DNA strands twined gradually to rod condensates. The possible reason for the condensation might be the masking of the electrostatic repulsion between DNA double strands by MC-LR The present study might provide useful information for the pathopoiesis mechanism of MC-LR. More, because the condensation of DNA could affect the progresses of gene expression and protein transcription, it may implicate another trend to explore the nosogenesis of MC-LR.