Salmon farmers are currently using high-energy feeds containing up to 35% fat; the fish's capability of fully utilizing these high-energy feeds has received little attention. Carnitine is an essential component in the process of mitochondrial fatty acid oxidation and, with the cooperation of two carnitine palmitoyltransferases (CPT-I and CPT-II) and a carnitine acylcarnitine transporter across the inner mitochondrial membrane, acts as a carrier for acyl groups into the mitochondrial matrix where beta-oxidation occurs. However, no reports are available differentiating between CPT-I and CPT-II activities in fish. In order to investigate the potential for fatty acid catabolism, the activities of key enzymes involved in fatty acid oxidation were determined in different tissues from farmed Atlantic salmon (Salmo salar), i.e., acyl-CoA oxidase (ACO) and CPT-I and CPT-II. Malonyl-CoA was a potent inhibitor of CPT-I activity not only in red muscle but also in liver, white muscle, and heart. By expressing the enzyme activities per wet tissue, the CPT-I activity of white muscle equaled that of the red muscle, both being >> liver. CPT-II dominated in red muscle whereas the liver and white muscle activities were comparable. ACO activity was high in the liver regardless of how the data were calculated. Based on the CPT-II activity and total palmitoyl-L-carnitine oxidation in white muscle, the white muscle might have a profound role in the overall fatty acid oxidation capacity in fish.