The molecular biomarkers in relation to environmental pollutants have become imperative research topic for environmental toxicology studies. In order to set up a series of simple, sensitive and exact monitoring systems for environmental pollution, several studies were carried out. The potential of oxygen free radicals and other reactive oxygen species (ROS) to damage tissues and cellular components in organisms was called oxidative stress. The balance between pro-oxidant endogenous and exogenous factors (i.e., environmental pollutants) and anti-oxidant defenses in biological systems has been used to assess the adverse effect of environmental pollutants, especially for oxidant damage of the different chemicals. The anti-oxidative defense systems and their sensitivity for oxidative stress are of great importance in environmental toxicology. Numerous studies on the effects of oxidative stress to organisms imposed by environmental pollutants were performed. The results indicated that the transition metals, polycyclic aromatic hydrocarbons, organophosphate and organochlorine pesticides, polychlorinated biphenyls, dioxins, and other xenobiotics could cause oxidative stress to organisms. These toxicants can stimulate a variety of toxicity effects, such as oxidative damage to membrane lipid, DNA and protein and changes to antioxidant enzymes. This review summarizes the current knowledge and advances in understanding such oxidative stresses. And the application of related molecular biomarkers in aquatic organisms was also discussed.