Highly unsaturated fatty acids (HUFAs) are essential for mammalian health, development and growth. However, most mammals, including humans, are incapable of synthesizing n-6 and n-3 HUFAs. Fish can convert C18 unsaturated fatty acids into n-6 and n-3 HUFAs via fatty acid desaturase (Fads), in which Fads2 is a key enzyme in HUFA biosynthesis. The allo-tetraploid common carp theoretically encode two duplicatedfads2genes. The expression patterns and desaturase functions of these two homologous genes are still unknown. In this study, the full length of thefads2aandfads2bwere identified in common carp (Cyprinus carpio). Expression analyses indicate that both genes were mainly expressed in the liver and the expression offads2bis higher thanfads2aat different developmental stages in carp embryos. Heterogenous expression and 3D docking analyses suggested that Fads2b demonstrated stronger ∆6 and ∆5 desaturase activities than Fads2a. The core promotor regions offads2aandfads2bwere characterized and found to have different potential transcriptional binding sites. These results revealed the same desaturase functions, but different activities of two homologues offasd2genes in common carp. The data showed thatfads2bplayed a more important role in HUFA synthesis through both expression and functional analyses.