Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we selectKelch-like(klhl) genes to study the evolution of the duplicated genes in the polyploidCarassiuscomplex, including amphidiploidC. auratusand amphitriploidC. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most ofCarassius klhlgenes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred duringCarassiusevolution. The lineage-specific expansion and biased retention/loss ofklhlgenes are also found inCarassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression ofklhlsin response toCarassiusherpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in threeC. gibeliogynogenetic clones. Finally, we find that mostC. gibelio klhlgenes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous forCgklhlgenes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.