Perfluorooctanoic acid (PFOA) and fluoranthene are organic pollutants with a widespread environmental occurrence. They are both present in the environment, and are known to concentrate and bioaccumulate in organisms, PFOA in general, fluoranthene in non-vertebrates. There are several studies showing toxic effects in marine organisms exposed to PFOA or fluoranthene. However, there is a lack of studies addressing the genotoxic effects of these contaminants. In this study, DNA damage and alteration of gene expression were investigated in blue mussels (Mytilus edulis) exposed in vivo to PFOA, fluoranthene and a mixture of the two. DNA strand breaks in haemocytes were analysed using the comet assay. The sensitivity of the assay was further improved by implementing the lesion specific enzyme FPG, to detect oxidative DNA damage. Gene expression analysis of Mt10, p53, RNA helicase and Krs, using RT-qPCR, were performed to assess the genotoxic effects of the compounds on gill tissue. There was substantial DNA damage in all exposure groups, including vehicle control and unexposed mussels. The amount of DNA damage in unexposed samples masked the effect of the exposure on DNA damage, and a comparison of exposed an unexposed mussels gave no clear results. No significant increase in DNA damage was observed in M. edulis compared to the vehicle control. Digestion with FPG caused a significant increase in oxidative DNA damage for mussels exposed to PFOA after 16 days, only. Gene expression analysis indicated oxidative stress as there was a significant up-regulation of p53, for mussel exposed to PFOA and mussels exposed to fluoranthene, and Krs for mussel exposed to PFOA. There was no significant alteration of Mt10 or RNA helicase. The results from the comet assay and RT-qPCR gave no indication of increased genotoxicity from a combined exposure to PFOA and fluoranthene. A high inter-individual variance in vehicle control (ethanol exposure only) was evident at the beginning of the experiment using the comet assay, as well as increased expression of Mt10 and p53. It is therefore possible that ethanol exposure induced genotoxic effects. Since the inter-individual variance was reduced after 8 and 16 days, and the up-regulation of p53 and Mt10 only was transient, it is possible that mussels adapted to the ethanol exposure.