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White Band Disease has caused unprecedented mortality in the Caribbean <em>Acropora</em> corals and resulted in their US Endangered Species listing. Highly disease resistant <em>A. cervicornis</em> genotypes exist, but we lack a basic understanding of the genetic underpinnings of coral disease resistance. Using transmission experiments and whole genome sequencing of 74 <em>A. cervicornis</em> genotypes from Florida and Panama, we identify ten genomic regions and 73 single-nucleotide polymorphisms (SNPs) that are strongly associated with disease resistance that includes in five genes involve coral immunity and pathogen detection. Polygenic scores calculated from our top 10 genomic loci demonstrate that simple genetic screens can accurately predict which corals will be highly disease resistant versus highly susceptible and then select highly disease resistant corals for nursery stocks and on-going restoration efforts.