The last 25 years have seen major advances in the field of mammalian genotoxicology, particularly with the advent of molecular methods, some of which have spilled over into the relatively new field of eco-genotoxicology, which aims to evaluate the impact of contaminants on the natural biota. Unlike mammalian genotoxicology, where the focus is centred on a limited number of model species, efforts in the marine field have generally lacked coordination and focus, with the result that progress has been somewhat slow and fragmented. However, it is recognized that at the DNA and chromosome levels, marine invertebrates express qualitatively similar types of induced damage to that found in higher organisms (e.g. point mutations, strand breaks and chromosomal aberrations). Given that many of these species (bivalve molluscs, crustaceans, polychaete worms, etc.) are linked directly or indirectly to the human food chain, this is an important reason why one should be concerned about their exposure to environmental mutagens and carcinogens, particularly as many of these organisms have the capacity to (i) transform these agents to biologically active metabolites and (ii) accumulate toxicants in their cells and tissues at concentrations several orders of magnitude above that found in the environment. This review covers the advantages and limitations of those cytogenetic and molecular assays that have been used to address the question of genotoxicity in the cells and early life stages of selected marine invertebrate species. It concludes with the recommendation for the adoption of standardized test procedures, leading to a tiered approach in future eco-genotoxicity testing.