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The soybean cyst nematode ( SCN ) resistance locus   R hg1  is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2‐kb unit contains four genes. One allele of   R hg1 ,   R hg1‐b , is responsible for protecting most  US  soybean production from  SCN . Whole‐genome sequencing was performed, and  PCR  assays were developed to investigate allelic variation in sequence and copy number of the   R hg1  locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2‐kb repeat unit were identified, and some   R hg1  alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the   R hg1  locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the   R hg1  genotype to be inferred using high‐density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess   R hg1  alleles. The regions surrounding the repeat show indications of non‐neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at   R hg1 .

Evolution and selection of R hg1, a copy‐number variant nematode‐resistance locus