Whilst the hybrids of F1 generations usually experience heterosis for fitness-related traits (including the resistance to parasites), post-F1 generations, due to Dobzhansky–Muller genetic incompatibilities, express numerous disadvantageous traits (including susceptibility to parasites). Genetic disruption in hybrids may also result from the broken system of cyto-nuclear coadaptation. Maternal backcrosses (each parent having with the same mtDNA of parents) and paternal backcrosses (each parent having with different mtDNA of parents) have the same nuclear genetic compositions, but differ in cytoplasmic genetic elements, affecting their viability and survival. Spring viraemia of the carp virus (SVCV), a disease with a serious economic impact in aquacultures, affects almost exclusively cyprinids, primarily common carp, and causes high mortality, whilst gibel carp is a less susceptible species. Our study was focused on the transcriptome profile analysis of head kidney to reveal differential gene expression in highly susceptible common carp, weakly susceptible gibel carp, and hybrid lines, hypothetizing that the patterns of differential gene expression will reflect hybrid heterosis in F1 generations and hybrid breakdown in backcrosses and F2 generations. We expected the differences in differential gene expression between maternal and paternal backcrosses to be in line with the hypothesis of broken cyto-nuclear coadaptation. Overall design: The pattern of differential gene expression revealed from the transcriptomic analysis of head kidney was linked to the resistance or susceptibility to SVCV infections in two pure species, C. gibelio and C. carpio, and their various generations of inter-specific hybrids. We evidenced hybrid heterosis for F1 generations of hybrids, mostly reflected by similarity in the down-regulation of DE genes classified within the viral infection disease category. High hybrid breakdown was documented throughout the transcriptomic analysis for paternal backcross generations and F2 generation of hybrids, confirming the broken system of cyto-nuclear coadaptation in those post-F1 generations. This evidence may support the role of intrinsic selection acting against inter-specific hybridization in freshwater fish. Total RNA was isolated from the head kidney of each fish specimen. For extraction, PureLink RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific) and on-column PureLink DNase treatment were used. In total, 70 samples from 3 dpi (by SVCV) sampling and from non-infected fish with an acceptable RIN (RNA integrity number – RIN > 7) were used for DNA library preparation.