The effects of ionising radiation (IR) present in aquatic environments have been observed principally in vertebrate species but the potential biological impacts for aquatic invertebrate species are less clear. It is important to determine the influence of IR as a pollutant causing DNA damage in invertebrates at the molecular level since this may serve as an early warning of future population level repercussions. In this study, the biological effects of the IR as an environemntal contaminant at the molecular level was investigated by studying the induction of DNA damage, measured as mRNA expression of DNA repair genes and comet damage, in experimentally- and environmentally-exposed mussels, M. edulis. The experimental exposure consisted of different IR doses (1, 2, 10 and 50 Gy) and sampling at different post-exposure time points (1hr, 4 and 7 days). The environmental exposure was investigated using mussels collected from a contaminated site (Ravenglass Estuary) and a reference site (Brighton Marina). Two new molecular biomarkers were developed and employed. The first involves Rad51, a key protein in resynthesis, catalyzing and transferring of strands between broken sequences and its homologues in double strand break (DSBs) damage. The second biomarker involved a cell cycle checkpoint protein, check point kinase 1 (Chk1). To explore the activation of Rad51 and Chk1 mRNA activity as a result of exposure to IR, Rad51 and Chk1 mRNA in M. edulis were partially isolated and characterized and a quantitative assay developed to measure their expression using real-time PCR. Experimental exposure of M. edulis to IR (1, 2, 10 and 50 Gy) resulted in a statistically significant increase in the levels of Rad51 transcripts. Chk1 mRNA expression levels, initially investigated in the experimental group, were altered following exposure to IR. In the samples collected from the environment, Rad51 mRNA expression levels were increased in Ravenglass M. edulis gonad samples compared with the reference samples from Brighton Marina. In contrast, Chk1 transcripts decreased in Ravenglass M. edulis gonad samples compared to Brighton samples. The observed effects, and the potential role of both Rad51 and Chk1 in the IR DNA damage response of mussels are discussed.