This study examines the potential effects of linseed oil as a total replacement for fish oil in the formulated diet of Arctic charr, brook charr and their reciprocal hybrids. Muscle fatty acid composition, growth performance and feed utilization were evaluated on four experimental groups submitted to two different dietary lipid sources (100% linseed oil or 100% fish oil). Growth performance, feed utilization, muscle lipids and protein content were not affected by dietary linseed oil. Lipid source significantly affected muscle fatty acid profile. The replacement of fish oil by linseed led to an average reduction in 20:5n3 and 22:6 n3 (25.5% and 18.4% respectively) and an increase in 18:3n3 (177%) (mean values calculated for the four experimental groups). Muscle fatty acid profile was primarily influenced by feed content. Hybridization between the closely related species did not appear to affect the expression of key enzymes for HUFA biosynthesis. Our results show that linseed can be used as a fish oil replacement in charr without any significant impact on growth, feed utilization or muscle lipid and protein content.