Chemicals with the potential to damage DNA are increasingly present in the marine environment; yet our understanding of the long-term consequences of DNA damage for populations remains limited. We explore the impact of paternal genotoxin exposure on the reproductive biology of two ecologically important free-spawning marine invertebrates: the polychaete Arenicola marina and the mussel Mytilus edulis. Males were exposed in vivo for 72 h to methyl methanesulfonate and benzo(a)pyrene and the impact on somatic cells and sperm assessed using the Comet assay. A strong correlation between DNA damage in somatic cells and sperm was observed after 24 h exposure (P < 0.001). Recovery in sperm was significantly lower than in coelomocytes after 72 h. The fertilization success of DNA-damaged sperm was unaffected, but a significant percentage of embryos derived from sperm with induced DNA damage exhibited severe developmental abnormalities within 24 h of fertilization with potential long-term consequences for population success. Further research is required to determine the mechanism by which paternal DNA damage causes disruption of development at this early stage.