Aquatic pollutants produce multiple consequences at organism, population, community and ecosystem level, affecting organ function, reproductive status, population size, species survival and thus biodiversity. Among these, carcinogenic and mutagenic compounds are the most dangerous as their effects may exert a damage beyond that of individual and may be active through several generations. The application of genotoxicity biomarkers in sentinel organisms allows for the assessment of mutagenic hazards and/or for the identification of the sources and fate of the contaminants. Micronucleus (MN) test as an index of accumulated genetic damage during the lifespan of the cells is one of the most suitable techniques to identify integrated response to the complex mixture of contaminants. MN assay is today widely applied in a large number of wild and transplanted aquatic species. The large majority of studies or programmes on the genotoxic effect of the polluted water environment have been carried out with the use of bivalves and fish. Haemocytes and gill cells are the target tissues most frequently considered for the MN determination in bivalves. The MN test was widely validated and was successfully applied in a large number of field studies using bivalves from the genera Mytilus. MN in fish can be visualised in different cell types: erythrocytes and gill, kidney, hepatic and fin cells. The use of peripheral erythrocytes is more widely used because it avoids the complex cell preparation and the killing of the animals. The MN test in fish erythrocytes was validated in laboratory with different species after exposure to a large number of genotoxic agents. The erythrocyte MN test in fish was also widely and frequently applied for genotoxicity assessment of freshwater and marine environment in situ using native or caged animals following different periods of exposure. Large interspecies differences in sensitivity for MN induction were observed. Further validation studies are needed in order to better characterise the different types of nuclear alterations and to clarify the role of biotic and abiotic factors in interspecies and inter-individual variability.