An eight-week feeding trial was conducted to evaluate the influence of an alternating linseed oil (LO) and fish oil (FO) feeding strategy in black seabream A. schlegelii (initial weight, 8.49 ± 0.01 g). Two isonitrogenous and isolipidic feeds were formulated to contain FO or LO, and used to enable three feeding strategy treatments termed FO (feeding the FO diet for 8 weeks), LO (feeding the LO diet for 8 weeks) and FO re-feeding (feeding LO for 4 weeks then FO for 4 weeks). Fish in the FO re-feeding and FO groups had significantly higher final body weights (FBW), weight gains (WG), specific growth rates (SGR) but lower muscle lipid content than fish in the LO group. In muscle, the FO re-feeding strategy restored eicosapentaenoic and docosahexaenoic acid contents to 82.67% and 83.84%, respectively, of those in fish fed the FO treatment. In addition, the FO re-feeding strategy significantly down-regulated the expression levels of genes related to long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis and lipogenesis, including fatty acyl desaturase (fads2), elongase of very long-chain fatty acids 4a (elovl4a) and sterol regulatory element-binding protein-1 (srebp-1) compared to fish fed the LO treatment. Similarly, the hepatic Srebp-1c concentration in fish in the FO re-feeding group was markedly lower than in fish in the LO treatment group. Expression of the lipid catabolism gene adipose triglyceride lipase (atgl) was up-regulated in fish in the FO re-feeding group compared with fish in the LO group. Overall, the present study indicated that a strategy of re-feeding FO following feeding LO for four-week promoted growth, mitigated lipid accumulation in muscle, and effectively restored muscle n-3 LC-PUFA levels in A. schlegelii.