Aquatic organisms living in coastal/estuarine areas show peroxisome proliferation after exposure to different environmentally relevant pollutants. In order to generate new tools to assess peroxisome proliferation in aquatic animals, peroxisomal enzymes were cloned using degenerate primers in the mussel Mytilus galloprovincialis and in the thicklip grey mullet Chelon labrosus. Fragments of catalase (CAT), thiolase (THIO), polyamine oxidase (POX) and xanthine oxidoreductase (XOR) were cloned and their expression pattern studied in different tissues by semi-quantitative RT-PCR. In mussels, CAT, THIO, POX and XOR were expressed in digestive gland, mantle and gills while in mullets CAT, THIO and POX were expressed in liver, spleen, brain, heart, muscle and gills. XOR was mainly expressed in liver and heart. Mature mullets showed the highest expression of peroxisomal enzymes in liver, spleen and brain, while in juveniles expression was mainly found in muscle tissues, liver and gills. Laboratory experiments of exposure to organic pollutants are being performed to study the usefulness of these tools to study peroxisome proliferation in pollution biomonitoring programmes.