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Most diploid freshwater and marine fish encode one <i>elovl5</i> elongase, having substrate specificity and activities towards C18, C20 and C22 polyunsaturated fatty acids (PUFAs). The allo-tetraploid common carp is hypothesized to encode two duplicated <i>elovl5</i> genes. How these two <i>elovl5</i> genes adapt to coordinate the PUFA biosynthesis through elongase function and expression divergence requires elucidation. In this study, we obtained the full-length cDNA sequences of two <i>elovl5</i> genes in common carp, named as <i>elovl5a</i> and <i>elovl5b</i>. Functional characterization showed that both enzymes had elongase activity towards C18, C20 and C22 PUFAs. Especially, the activities of these two enzymes towards C22 PUFAs ranged from 3.87% to 8.24%, higher than those in most freshwater and marine fish. The Elovl5a had higher elongase activities than Elovl5b towards seven substrates. The spatial-temporal expression showed that both genes co-transcribed in all tissues and development stages. However, the expression levels of <i>elovl5b</i> were significantly higher than those of <i>elovl5a</i> in all examined conditions, suggesting that <i>elovl5b</i> would be the dominantly expressed gene. These two genes had different potential transcriptional binding sites. These results revealed the complicated roles of <i>elovl5</i> on PUFA synthesis in common carp. The data also increased the knowledge of co-ordination between two homoeologs of the polyploid fish through function and expression divergence.