Few studies have described the molecular response of mollusk larvae to heavy metal exposure. We investigated the response of Chilean scallop Argopecten purpuratus post-larvae to copper exposure under experimental conditions. Post-larvae were maintained with and without copper stress in tanks containing netlon collectors with biofilms that were formed by the bacterium Halomonas sp. and the diatom Amphora sp., known to increase larval settlement. We focused on the analysis of the differential expression patterns of genes associated with copper response. A suppression subtractive hybridization method was used to identify copper-specific up- and down-regulated genes in the post-larvae following 4 days and 8 days exposure to 2.5 and 10 microg/l Cu(+2). This method revealed 145 different sequences corresponding to 10 major physiological functions. The expression of 15 potentially regulated genes was analyzed by real-time PCR in post-larvae at different sampling times during the copper stress. The genes chosen were alpha tubulin, elongation factor 1-alpha (EF1A), tributylin binding protein type 1 (TBT), NADH dehydrogenase subunit 2 (NADH2), cavortin, glutathione peroxidase (GPx), ferritin, heat shock protein 70 (HSP70), Pam highwire rpm1 (Phr1), insulin-like growth factor 1 (IGF1), cellulase, and ribosomal proteins: L18, L44, S3a and S15. This study contributes to the characterization of potential genetic markers that could be used in future environmental monitoring and to explore new mechanisms of stress tolerance in marine mollusk species, especially in early stages of development.