Energy intake and genetic background are major determinants of muscle fat content in most animals, including man. We combined genetic selection and dietary energy supply to study the metabolic pathways involved in genetic and nutritional control of fat deposition in the muscle of rainbow trout (Oncorhynchus mykiss). Two experimental lines of rainbow trout, selected for lean (L) or fat (F) muscle, were fed with diets containing either 10 or 23 % lipids from the first feeding, up to 6 months. At the end of the trial, trout exhibited very different values of muscle fat content (from 4·2 to 10·1 % wet weight). Using microarrays made from a rainbow trout multi-tissue cDNA library, we analysed the molecular changes occurring in the muscle of the two lines when fed the low-energy or high-energy diet. The results from microarray analysis revealed that eleven metabolism-related genes were differentially expressed according to the diet while selection resulted in expression change for twenty-six genes. The most striking observation was the increased level of transcripts encoding the VLDL receptor and fatty acid translocase/CD36 following both the high-fat diet and upward selection for muscle fat content, suggesting that these two genes are relevant molecular markers of fat deposition in the white muscle of rainbow trout.