As a key factor in cholesterol metabolism, Apolipoprotein E is participate in lipoprotein transport and gonadal development. To understand function of ApoE, the cDNAs of allotetraploid and their parents-red crucian carp and common carp were cloned and sequenced. The full length of allotetraploid, red crucian carp and common carp ApoE cDNAs were 1393 bp, 1384 bp and 1396 bp, respectively. All the cDNAs encode 281 amino acids. Based on alignment result, ApoE of allotetraploid is more similar with common carp than red crucian carp. Meanwhile, besides characters inherited from parents, allotetraploid shows specific mutation in ApoE. By constructing phylogenetic?tree using Mega software, the phylogenetic?tree of ApoE was consistent with taxonomy: cyprinid fish are clustered together rather than other vertebrates. Realtime-PCR analysis indicated that the expression patterns of ApoE in allotetraploid, common carp and red crucian carp are similar. All the tissues had ApoE expression. The highest expression was in spleen. This research gave information in gene variation in the process of allotetraploid evolvement and lipid metabolic mechanism of fish.