Update publication information. Heterosis is a complex biological phenomenon in which hybridization exhibits superior phenotypic characteristics. The underlying molecular basis for heterosis, particularly for fishes, remains elusive. The utilization rate of fish heterosis far exceeds our understanding of it on a theoretical level. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we characterized mRNA-seq, miRNA-seq, and proteomes of Pelteobagrus fulvidraco, P. vachelli, and the hybrid yellow catfish Huangyou-1 (P. fulvidraco ♀×P. vachelli ♂) livers using next-generation sequencing technologies and tandem mass tags. Our results show that the nonadditive, homoeologue expression bias and expression level dominance pattern were readily identified in transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. At the same time, a number of miRNA-mRNA-protein pairs were found and validated by qRT-PCR and parallel reaction monitoring assays.