The fluctuating thermal nature of the marine environment induces physiological changes in ectotherms that require molecular and gene expression adjustments [1]. Comparative gene expression studies can be used to characterize these adjustments and lead to a better understanding of organismal responses to environmental change. Gene expression datasets can be clustered into groups of genes that represent different compartments of cellular function, and changes in the expression of genes from these clusters can be used to formulate hypotheses as to how different tissues and whole organisms respond to particular biotic or abiotic stresses. Few studies have addressed changes in gene expression in response to temperature variation on marine organisms. Alterations in gene expression have been observed in fish acclimated to constant temperatures and then exposed to daily temperature fluctuations [2] or to a strong heat stress [3]. However, few molecular investigations have focused on the thermal stress response in marine invertebrates [4,5], particularly in the context of global changes and the potential effects on marine invertebrates [6,7].The Pacific oyster Crassostrea gigas is a eurythermic bivalve mollusc that colonizes most of the western coast of Europe. This species prefers sheltered estuarine waters, where it is found in intertidal and shallow subtidal zones. Within their geographic range, oysters typically experience and respond to seasonal temperatures ranging from 4 to 24°C [8]. In the coldest regions inhabited by C. gigas, such as Brittany, Groups of oysters (Crassostrea gigas) were exposed to 25°C for 24 days (controls to 13°C) to explore the biochemical and molecular pathways affected by prolonged thermal stress. This temperature is 4°C above the summer seawater temperature encountered in western Brittany, France where the animals were collected. Suppression subtractive hybridization was used to identify specific up-and downregulated genes in gill and mantle tissues after 7-10 and 24 days of exposure. The resulting libraries contain 858 different sequences that potentially represent highly expressed genes in thermally stressed oysters. Expression of 17 genes identified in these libraries was studied using real-time PCR in gills and mantle at different time points over the course of the thermal stress. Differential gene expression levels were much higher in gills than in the mantle, showing that gills are more sensitive to thermal stress. Expression of most transcripts (mainly heat shock proteins and genes involved in cellular homeostasis) showed a high and rapid increase at 3-7 days of exposure, followed by a decrease at 14 days, and a second, less-pronounced increase at 17-24 days. A slow-down in protein synthesis occurred after 24 days of thermal stress.Abbreviations CTSL, cathepsin L; EST, expressed sequence tag; HYPK, Huntingtin-interacting protein K; HSP, heat shock protein; LDH, lactate dehydrogenase; MTA-1, metastasis-associated protein 1; SSH, suppression substractive hybridization.