Abstract: The full-length cDNA of delta 6 fatty acid desaturase(△6FAD)in Trachinotus ovatus was cloned by RACE(Rapid Amplification of cDNA Ends), and the sequence structure of the gene and protein was determined through bioinformatics analysis. RT-PCR(Real-time PCR)was employed to analyze its expression differences in tissues under different temperatures and the expression patterns in low temperature. Ultimately, the results indicate that full length of cDNA sequence of △6FAD in T. ovatus is 1 908 bp, of which has 3' non-coding region 431 bp, 5' non-coding region 135 bp, and open reading frame 1 329 bp that encodes 442 amino acids. The protein is hydrophobic without signal peptide, and containing abundant protein secondary structure, typical histidine cluster motifs in this family, and cytochrome b₅ domain. Phylogenetic results from the BLAST protein database reveal that the deduced amino acid sequence of △6FAD of T. ovatus is highly homologous with Lates calcarifer and Rachycentron canadum：lowly homologous with Scophthalmus maximu, Thunnusthynnus and Epinephelus coioides：but little homologous with Danio rerio, Mus musculus and Homo sapiens. RT-PCR results manifest that gene expression of △6FAD is significantly correlated with temperature and stress time in environment, the expression level of the gene at first slowly decreases, then rapidly rises as temperature lowering in the experiment of temperature gradient. However, there is different expression pattern in different low-temperature environment：for example, at 13℃ the gene expression of △6FAD increases to its original level after first decreasing with time：and while at 16℃ and 19℃ it is gradually decreasing with time, i.e., feedback adjustment way.

Key words: Trachinotus ovatus, delta 6 fatty acid desaturase, cDNA cloning, low temperature stress