Abstract: To investigate the effects of linseed oil and soybean oil on fatty acid composition and Δ6Fad gene expression in liver and muscle of large yellow croaker, three defined diets were made with fish oil (FO), soybean oil (SO) and linseed oil (LO) as fat sources for a 10 weeks experiment on floating cages. Results indicated that the weight gain rate, feed efficiency ratio and specific growth rate of FO group was significantly higher than LO group and SO group (P<0.05), and no significant difference in survival rate,HSI and VSI (P>0.05) were observed among groups. The fatty acid was changed and the relative content of LC-PUFA (Long chain-polyunsaturated fatty acid) reduced significantly (P<0.05) in liver and muscle when fish oil was replaced by linseed oil and soybean oil, but there was no significant difference between linseed oil treatment and soybean oil treatment (P>0.05). The relative content of n-3 LC-PUFA in muscle was more than that of liver (P<0.05). SO and LO induced the Δ6Fad expression 7.6 and 6.5 times in liver and 2.2 and 2.8 times in muscle respectively. Results suggest that the replacement of fish oil by linseed oil and soybean oil had negative effect on fish performance possibly via lipids metabolism.