Molecular biomarkers refer to specific genes and/or its products present in ecosystems which have been exposed to physic or chemical alterations as a result of anthropogenic activities. These molecules are useful to estimate both change and spread of the damage level. The studies of DNA specific sequences, gene expression and proteins production allow to understand the consequences of the presence of specific pollutants or its mixtures in different ecosystems, but mainly in aquatic environments. To date, different gene targets have been used to understand the consequences derived by the introduction of specific pollutants into the environment and serve as excellent tools for environmental toxicology studies. In this review, some of the most commonly reported molecular biomarkers used to monitor the environmental impact in aquatic ecosystems and the pertinent considerations when they are used in environmental risk assessment studies are described.