Hydrocarbon contamination perturbs the metabolism of the marine bivalve Crassostrea gigas. To understand the response of this organism to hydrocarbon exposure, a suppression subtractive hybridisation method was employed to characterise up- and down-regulated genes during hydrocarbon exposure. The number of differentially expressed gene sequences obtained via this method was 258. The expression of genes involved in hydrocarbon detoxification (cytochrome p4501A1-like protein, cytochrome b(5), flavin-containing monooxygenase 2 and glutathione S-transferase omega class), protection against oxidative stress (copper/zinc superoxide dismutase) and cell protection (heat shock protein 70 family) was analysed by RT-PCR. An increase in the mRNA level of all genes studied was observed. A quantification of HSP70 by Enzyme Linked Immunosorbent Assay (ELISA) showed a significant increase of this protein during exposure. This study provides a basis for studying hydrocarbon detoxification processes in marine bivalves, especially C. gigas.