This study was carried out to investigate the effect of feeding diets containing herring or anchvoy oil, on flesh quality parameters of Atlantic salmon (Salmo salar). Two extruded experimental diets with the same basal composition but one coated with herring oil and the other with anchovy oil, were each fed during 24 weeks to salmon with an average initial weight of 1.8 kg. Salmon grew to a final weight of 3.9 kg. Growth, condition factor and biometric parameters were not affected by the dietary treatment. No significant differences were found for intramuscular fat. Monounsaturated fatty acid (MUFA) concentrations were highest in the group fed the diet containing herring oil, in both neutral and polar lipids, while the group fed the diet containing the anchovy oil showed a higher concentration of n-3 fatty acids in both fractions of intramuscular lipids. The n-3/n-6 ratio was higher in the neutral lipid fraction of fish fed the southern hemisphere oil, while no significantly differences were found for the polar lipid fraction. No differences were found on muscle α-tocopherol levels. Muscle homogenates from fish fed the anchovy oil showed the highest thiobarbituric acid reactive substances (TBARS) after 9 days of storage. However no differences were found between groups on the induced oxidation tests. It is concluded that the origin of the fish oil has no effect on growth perfomance, but there is a marked effect on fatty acid composition and susceptibility to lipid oxidation.