In November 2002 the tanker Prestige released more than 60,000t of a heavy fuel oil which spread over Galician waters and the Biscay Bay, affecting coastal ecosystems. Polycyclic aromatic hydrocarbons are the main components of the Prestige fuel oil and induce biotransformation metabolism and peroxisome proliferation in marine organisms. In vertebrates, this later response involves peroxisome proliferator-activated receptors (PPARs), transcription factors belonging to the nuclear receptor superfamily, that act upon heterodimerization with the retinoid X receptor (RXR). In order to assess the possible biological effects of the Prestige oil spill in the Biscay Bay, male and female juvenile and adult European hakes Merluccius merluccius were sampled in June and December 2004 and 2005. PCR screening of hake liver cDNA with degenerate primers resulted in cloning and sequencing of cDNA fragments of PPARα (1011bp), PPARγ (812bp), RXR (270bp) and of the PPARα target gene palmitoyl-CoA oxidase (AOX1, 792bp). Fragments of another 9 toxicologically relevant genes were also cloned and sequenced. PPARα mRNA expression was not significantly different among groups. In juvenile females transcription of PPARγ, RXR and AOX1 significantly increased in June 2005 when compared to June 2004. In adult males levels of AOX1 decreased in the same period. AOX1 and 7-ethoxyresorufin O-deethylase (EROD) activities, measured as exposure biomarkers, differed between years only in males sampled in June. EROD activity was higher in 2004 than in 2005 in adults, whereas both juvenile and adults showed higher AOX1 activity in 2005. The lack of historical data previous to the accident or in areas not affected by the accident did not allow to relate observed variations in gene transcription levels and enzyme activities to the Prestige oil spill. Reported data could be useful for comparison purposes for future studies in European hake and contributes gene sequence information relevant for future toxicological studies.