Abstract
While haplotype‐specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed‐haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba ( Bahaba taipingensis , Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame‐shifting variants as the most deleterious type, followed by mutations in the 5′‐UTR, 3′‐UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high‐impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter‐haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype‐resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.