Mutagenic pollution of environment is a global and important problem. This includes marine environment. Although many mutagenicity assays have been developed, there are specific problems with testing marine water and sediments for mutagenic contamination. One of them is the fact that most of genetically modified strains used in commonly available microbiological mutagenicity assays, like Escherichia coli or Salmonella, survive relatively poorly in marine waters, especially those of higher salinity. Thus, alternative assays have been developed, in which bacteria occurring naturally in marine habitats are employed. These assays, reviewed in this article, appear to be useful in testing not only marine samples but also can be used in other approaches, which involve detection and estimation of the amount of mutagenic compounds.