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Δ6 fatty acyl desaturase (Δ6Fads2) is regarded as the first rate-limiting desaturase that catalyzes the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFA) from 18-carbon fatty acid in vertebrates, but the underlying regulatory mechanism of <i>fads2</i> has not been comprehensively understood. This study aimed to investigate the regulation role of <i>fads2</i> subjected to fatty acid in large yellow croaker and rainbow trout. In vivo, large yellow croaker and rainbow trout were fed a fish oil (FO) diet, a soybean oil (SO) diet or a linseed oil (LO) diet for 10 weeks. The results show that LO and SO can significantly increase <i>fads2</i> expression (<i>p</i> < 0.05). In vitro experiments were conducted in HEK293T cells or primary hepatocytes to determine the transcriptional regulation of <i>fads2.</i> The results show that CCAAT/enhancer-binding protein α (C/EBPα) can up-regulate <i>fads2</i> expression. GATA binding protein 3 (GATA3) can up-regulate <i>fads2</i> expression in rainbow trout but showed opposite effect in large yellow croaker. Furthermore, C/EBPα protein levels were significantly increased by LO and SO (<i>p</i> < 0.05), <i>gata3</i> expression was increased in rainbow trout by LO but decreased in large yellow croaker by LO and SO. In conclusion, we revealed that FO replaced by LO and SO increased <i>fads2</i> expression through a C/EBPα and GATA3 dependent mechanism in large yellow croaker and rainbow trout. This study might provide critical insights into the regulatory mechanisms of <i>fads2</i> expression and LC-PUFA biosynthesis.