Estuaries are semi-enclosed marine areas with water short residence times. Estuary ecosystems show a higher susceptibility to contamination, as historically these sites are linked to urban and industrial development. Polycyclic aromatic hydrocarbons (PAH) are ubiquitous contaminants present in high quantities in these marine environments. Chemical analyses of sediments provides information regarding PAH pollution levels but not a direct measure of the toxicological effects attributed to these contaminants. Samples of sediments and of two bivalve species, Cerastoderma edule and Mytilus galloprovincialis, were collected from two locations (Corcubión and A Concha) in an estuary from northwestern Spain. The PAH levels in sediment and bivalve species and possible sources were determined. A moderate level and a low level of pyrogenic PAH contamination were observed in Corcubión and in A Concha, respectively. Genotoxic damage was evaluated in gills and hemocytes from mussels and cockles by means of the comet assay. DNA damage measured as DNAt values showed a reliable relationship with pollution load levels of the two sampling sites. The higher sensitivity of C. edule compared to M. galloprovincialis enables one to recommend including another species coupled with mussels for biomonitoring estuarine environments.