Malathion is a highly toxic organophosphate insecticide, being one of the most widely used in the world and is generally used for insect control in food production. Thus, ecotoxicological studies have been used to verify its toxic effects on aquatic organisms, such as Daphnia magna and biomarkers, as the comet assay. The comet assay is a microgel electrophoresis method for the detection and quantification of DNA strand breaks in individual cells. Cells were obtained from Daphnia magna after disaggregation of newborn organisms, exposed at concentrations of 0.23 μg L-1 and 0.47 μg L-1 for 48 h. Malathion has shown to cause damage to DNA of the exposed organisms. It was also observed the need of further studies to standardize the comet assay technique for Daphnia magna, once methodologies used present several differences.