Global changes in the marine environment and the continuing disposal of genotoxic xenobiotics are increasing the importance of environmental pollution monitoring and of biomonitoring programs. Current approaches focus on investigations at regional and local levels in an attempt to precisely define the nature and extent of any potential environmental crisis. We have initiated, for the first time, a long-term biomonitoring program focusing on the Croatian coast of the Adriatic Sea to contribute to a more detailed understanding of marine genotoxic effects using the mussels Mytilus galloprovincialis Lam., collected along the eastern Adriatic coast over a period of five years (1998-2002), as a key test organism. The integrity of DNA in its gill homogenate was examined by the Fast Micromethod. The strand scission factor (SSF) values, as a measure of DNA integrity, DNA damage or incomplete repair have been used for the ranking of sampling sites with respect to significant genotoxic stress due to the influence or effects of genotoxic xenobiotics. The region of Split (Kastela Bay) proved to be the area with the heaviest load of genotoxic agents. The investigation of harmful effects in the ecosystem based on biomonitoring of genetic and other agents, not only on local levels but also on a wider scale, is considered as an important step in marine environmental management.