Groups of oysters (Crassostrea gigas) were exposed to 25 degrees C for 24 days (controls to 13 degrees C) to explore the biochemical and molecular pathways affected by prolonged thermal stress. This temperature is 4 degrees 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.