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Potato is the most widely consumed tuber crop globally, yet breeding progress is limited by its complex, highly heterozygous, and often tetraploid genome. Traditional clonal propagation increases costs and disease risks, while the lack of inbred lines makes hybrid breeding difficult. The Upotato Plan aims to transform potato into a seed-propagated diploid crop that can be improved through modern hybrid breeding strategies. However, hidden deleterious mutations in the heterozygous genome have posed a major obstacle. To address this, we assembled a phased pangenome using 31 genetically diverse diploid potato accessions, including wild species and indigenous cultivars. This resource reveals extensive haplotype diversity and enables accurate detection of deleterious single nucleotide polymorphism (dSNPs) and deleterious structural variants (dSV). Notably, we discovered a “broken window” effect in the genome, where deleterious SNPs accumulate near harmful structural variants, compounding genetic burden. To reduce this load, we computationally designed “ideal haplotypes” with minimal harmful mutations, offering a powerful framework for precise parental selection and accelerated breeding. Our work demonstrates that phased pangenomes are essential for understanding potato genomic diversity and for guiding next-generation breeding strategies that can overcome long-standing barriers in potato improvement.