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Abstract Powdery mildew outbreaks, caused by Podosphaera xanthii, cause reduced watermelon yields as the plants produce fewer and smaller fruits due to premature leaf senescence. The reduced leaf canopy can decrease fruit quality due to sun scalding. Sources of powdery mildew tolerance were previously identified by screening the USDA Citrullus germplasm collection with P. xanthii races 1 W and 2 W. However, not all gene loci associated with tolerance to race 2 W have been identified and markers tightly linked to such loci have not been developed. We employed a bulked segregant analysis approach using historical data from the USDA Germplasm Resource Information Network for an extreme-phenotype genome-wide association study (XP-GWAS) of tolerance to P. xanthii race 2 W in Citrullus accessions (N = 1,147). XP-GWAS identifies variants that segregate between pools of individuals chosen from the extremes of a phenotypic distribution from a diversity panel. Whole-genome resequencing of 45 individuals bulked from tolerant and susceptible extremes resulted in 301,059 high-quality biallelic SNPs. Two adjacent SNPs on chromosome 7 were significantly associated with P. xanthii race 2 W tolerance in the bulks and two additional SNPs had a strong signal in the XP-GWAS analysis. Kompetitive Allele-Specific PCR (KASP) markers were designed for sixteen SNPs across the three genomic regions. The KASP markers were validated by genotyping 186 accessions from the extremes of the disease response distribution of the Citrullus collection. Analysis of variance determined that thirteen of the markers were significantly associated, with the best marker in each region explaining 21–31% of the variation in powdery mildew tolerance.