The variegated scallop Mimachlamys varia (Linnaeus, 1758) lives in soft sediments of the subtidal zone and is known to accumulate contaminants. Previous ecotoxicological studies have indicated that this species is a good candidate for biomonitoring along the French Atlantic coast. The species is a potential model for evaluating the effects of chemical pollution at the population genetic level, but information on its genetic structure at this spatial scale is lacking. To fill this gap in knowledge, variegated scallops were collected in fourteen sites of contrasting level of pollution over a distance exceeding 1,000 km on the French Atlantic coast. We analysed sequences of the mitochondrial gene coxI from 484 variegated scallops. The genetic data showed no evidence of population structure among these sites. Differences in genetic diversity were observed among sampling sites, but these differences were not linked to habitat quality in terms of inorganic contamination.