Marine pollution affects all life processes in aquatic organisms. The genotoxic effect of pollution on the mussel Crenomytilus grayanus was assessed. Bivalves were collected from the ‘clean’ (Vostochnaya Cove) and polluted (Nakhodka Bay) areas in the Peter the Great Bay. The degree of DNA damage in C. grayanus was determined by alkaline comet assay as mean percentage of DNA in tail, and the genetic damage index was calculated. Our results indicate that almost one-third of DNA in cells of gills and digestive gland of C. grayanus inhabiting the Nakhodka Bay had destructive changes compared to the individuals of this species from the Vostochnaya Cove. This study has shown that chronic pollution of the aquatic environment causes destructive changes to DNA in gill and digestive gland cells of C. grayanus.