Fatty acids are a vital energy source in fish and are of significant importance to their physiological wellbeing. Amago salmon (Oncorhynchus masou ishikawae) transgenic for a growth hormone (GH) show both accelerated growth and altered fatty acid composition and content in liver tissues. In particular, they show a decrease in saturated fatty acids and monounsaturated fatty acids, and an increase in polyunsaturated fatty acids except for docosahexaenoic acid (22:6n−3) and eicosapentaenoic acid (20:5n−3). Furthermore, transgenic fish have decreased levels of serum glucose, triacylglycerol and an increase in 3-hydroxybutyric acid, generally considered a starvation marker. As liver tissue is physiologically connected to muscle tissue, here we examined the effects of GH transgenesis on fatty acid contents in muscles of homozygous and heterozygous GH transgenic fish. The major monounsaturated fatty acids oleic acid (18:1n−9) and palmitoleic acid (16:1n−7) were slightly higher in the control, whereas polyunsaturated fatty acids, except 22:6n−3 and 20:5n−3, were significantly greater in the transgenic fish (P<0.05), similar to the results from the liver. However, by contrast to the liver, the major saturated fatty acids palmitic acid (16:0) and stearic acid (18:0) and polyunsaturated fatty acids (22:6n−3) and (20:5n−3) were significantly higher (P<0.05) in the transgenic fish than in the controls.