Abstract: To investigate the resistance differences against Carassius auratus herpesvirus (CaHV) among different gynogenetic clones of gibel carp (Carassius gibelio) and identify potential antiviral resistance-related genes, seven gynogenetic clones and performed microsatellite identification on their maternal individuals. These seven clones were established, including three Fangzheng clones (FZ1, FZ2, and FZ3), one Poyang clone (PY), one Pengze clone (PZ), along with two control clones: the highly resistant clone H and the susceptible variety allogynogenetic gibel carp “CAS III” (clone A⁺). Subsequently, artificial infection experiments with CaHV were conducted on these clones. The survival rates, ranked from highest to lowest, were: H (100%)>FZ2 (95%)>PY (40%)>FZ1 (20%)=FZ3 (20%)=PZ (20%)>A⁺ (10%). At 48h post-infection, histological observations revealed that the liver cells of the highly resistant clones FZ2 and H exhibited tighter cellular arrangements and significantly lower expression levels of CaHV gene orf72, indicating low viral load. In contrast, susceptible clones FZ1, FZ3, PZ, and A⁺ displayed swollen liver cells and elevated orf72 expression, suggesting high viral load. Additionally, whole-genome resequencing of 10 offspring from each clone identified 35278852single nucleotide polymorphism loci. Genome-wide association study mapped 63 genomic regions associated with disease resistance traits, encompassing 213 annotated genes. Integrative analysis with transcriptomic data and qPCR validation identified 11 potential antiviral resistance-related genes. This study not only identifies superior germplasm with high resistance to CaHV but also screens potential genes for disease resistance, laying a foundation for antiviral disease-resistant breeding in gibel carp.