A library of expressed sequence tags (ESTs) was constructed by the use of suppression subtractive hybridization polymerase chain reaction (SSH PCR) technique from the marine copepod Calanus finmarchicus. Samples used were from controls (seawater, 10 degrees C) and exposed (sublethal mixture) individuals. The sublethal exposure regime consisted of a mixture of mono ethanol amine (MEA), water-soluble fractions of oil (WSFs), copper (Cu) and elevated temperature (17 degrees C). The resulting 189 unique ESTs consisted of 127 putatively up-regulated genes and 54 putatively down-regulated genes. Annotation analyses revealed altered expression of a wide variety of genes, among these putative heat shock protein 90 (HSP-90), antioxidants (thioredoxin reductase, glutathione peroxidase) and cytochrome P450 enzymes. In addition, sequences showing high similarity to enzymes involved in fatty acid metabolism, energy metabolism and amine handling were found further confirming the effects of the exposure. The annotated sequences are discussed in relation to the present exposure as well as known physiological mechanisms known in C. finmarchicus and related copepod species. The sequenced ESTs from our C. finmarchicus library will provide an excellent tool for future studies on this species, both from a toxicogenomic and systems biology point of view.