Abstract: The full-length Δ6FAD cDNA of mirror carp (Cyprinus carpio) was cloned by reverse transcript PCR (RT-PCR) and rapid amplification of cDNA ends (RACE) to study the regulatory role of Δ6 fatty acid desaturase in the biosynthesis of highly unsaturated fatty acid (HUFA). The cDNA for Δ6FAD gene was 1 446bp in full length including an ORF of 1 332 bp encoding a peptide with 444 amino acids (accession no.KJ576791). The protein sequence contained all the characteristics of microsomal fatty acid desaturases, including 3 histidine boxes, 2 transmembrane regions，and a cytochrome b5 domain．The protein sequence was characterized by microsomal fatty acid elongases and sharing 69% ~92.0% sequence identity with the Δ6 desaturase gene in other fish. The phylogenetic tree showed that it clustered closely into freshwater fishes. The expression of the enzyme gene in different tissues of mirror carp was detected by real-time quantity PCR (RT-qPCR), the maximum in the heptopancreas, followed by muscle, and the minimum in blood. There was higher expression level of Δ6FAD in liver than in other tissues, Indicating that heptopancreas is the main tissue of HUFA biosynthetic mechanism, with the minimal expression level of Δ6FAD in blood. The findings will be helpful for clarifying the HUFA biosynthetic mechanism in mirror carp and for the development of method in enhancing such ability.