Bioassay methods currently used to assess the toxicity of effluents, transitional and marine waters measure endpoints such as larval immobilisation or mortality, however, they offer limited data regarding important sub-lethal effects, including genotoxicity. The metaphase chromosome aberration (CAb) assay is routinely used in mammalian systems for testing samples for genotoxicity. In the current study, an in vivo CAb test system has been developed and optimised for use with the early (embryo-larval) life stages of the Pacific oyster Crassostrea gigas, a species used routinely in both effluent hazard assessment and marine environmental monitoring programmes. The method was validated with two reference mutagens: Methylmethanesulfonate, a direct acting mutagen; and benzo[a]pyrene an indirect acting reference mutagen.