Independent of their nutritional condition, Pekin ducks always exhibit higher i.m. fat content than Muscovy ducks. To understand this difference between species, the expression level of genes involved in lipid metabolism was analyzed in the pectoralis major muscle of Pekin and Muscovy ducks ad libitum-fed or overfed. The lipoprotein lipase (LPL) gene expression was not different between species and not influenced by overfeeding. The protein content for LPL was higher in Pekin ducks than in Muscovy ducks when birds were ad libitum-fed, whereas in overfed ducks, we found no difference between species. Adipocyte fatty acid-binding protein (A-FABP) gene expression and protein content were higher in Pekin ducks than in Muscovy ducks for each nutritional condition (suggesting a higher intracellular transport within i.m. adipocytes of fatty acids mainly provided by liver for this species). Overfeeding did not affect the expression of genes involved in oxidation [carnitine palmitoyl transferase 1A (CPT1A), cytochrome-c oxidase 4 (COX4), succinyl-coenzyme A:3-ketoacid coenzyme A transferase (SCOT)] but increased the expression of fatty acid synthase (FAS) involved in lipogenesis. For all nutritional conditions, Pekin duck exhibited higher expression levels of CPT1A, COX4, SCOT, and FAS than Muscovy ducks. Results for mRNA SCOT suggested that the muscles of Pekin ducks use ketone bodies as an energy source. In conclusion, i.m. lipogenesis could contribute to the i.m. fat, particularly in Pekin ducks.