The sea is becoming increasingly polluted by the sum of the many substances that enter the marine environment. A significant group of substances affecting marine organisms are genotoxic. These are the substances damaging structure and function of a DNA molecule. Measured DNA damage indicates that an interaction has occurred between the pollutant and the organism. Therefore, the measurment of DNA damage is essential to determine genotoxic risk. For the purpose of determining DNA damage in a bioindicator organism, mussels (Mytilus galloprovincialis) used to monitor marine ecosystem pollution, the following methods are being applied: alkaline filter elution, rapid micromethod, comet assay and flow cytofluorimetry. Alkaline filter elution and comet assay are time-consuming and tedious methods, while the rapid micromethod enables the analysis of DNA integrity in multiple samples in short time (96 samples over 2 hours) and is therefore suitable for monitoring. All three methods analyze the same types of DNA damage: single-stranded and double-stranded breaks, cross-linking of DNA strands and DNA strands and proteins, intercalation between bases, formation of alkaline labile sites, etc. Flow cytofluorimetry is suitable for cell cycle analysis of larger number of sumples but the necessary instrument is expensive. Therefore, it is recommended to use fast micromethod for biomonitoring as a more cost effective method or expensive flow cytofluorimetry, and the choice depends on the genotoxic effect.