Coastal waters are burdened with different contaminants of anthropogenic origin due to intensive urbanisation and economical development. Bays, semi-enclosed areas with limited water renewal ability, are particularly endangered by contaminant inputs. Kastela Bay (Dalmatia, Eastern Adriatic) has earlier been identified as an area loaded with diffuse sources of pollution, including genotoxic agents. However, there is lack of data on the effects of these contaminants on the local marine fauna. The aim of this study was to assess genotoxic impacts in Kastela Bay and the neighbouring Trogir Bay using the micronucleus test and Comet assay with mussel (Mytilus galloprovincialis) haemocytes. Native and caged mussels were included in the studies. Our results confirmed that mussels in Kastela and Trogir Bays are affected by genotoxic contaminants. In addition to mussels from the most known polluted site (Vranjic), there was evidence for genotoxic effects in mussels collected at other locations. The response in the micronucleus test and the Comet assay differed somewhat between sites, the latter apparently being more sensitive, but the two methods complement each other and it is therefore desirable to use them both in monitoring the impacts of genotoxic pollution in coastal waters.