Micronuclei tests is a system of mutagenicity testing used for determining the pollution and chemicals causing changes in DNA fragments such as micronuclei in the cytoplasm of interphase cells. Damage caused on the DNA by genotoxic pollutants is the first consequence occurring in the aquatic organisms. Thus, it was attempted to determine whether pollution affected the erythrocytes and gills of fish Gobius niger and haemolymph and gills of mussels Mytilus galloprovincialis living in Izmir Bay at the level of DNA by the means of micronuclei (MN) test. Organisms used in the MN test were collected from seven locations (Alsancak, Alaybey Shipyard, Karsiyaka, Bostanli, Goztepe, Konak and Pasaport) which are known as the most polluted part of inner Bay of Izmir (Western Coast of Turkey). According to the results of the present study, frequency of MN was found at high level in Alaybey Shipyard and Pasaport where wastes from existing dockyard contributed to high level of pollution. In conclusion, this study indicates that the micronuclei test gives sensitive results in monitoring the pollution, especially the pollution of harbor, and thus it might be used as standard method in regular monitoring of pollution of coastal ecosystem.