Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is estimated to causes the greatest losses of any soybean [Glycine max (L.) Merr.] disease worldwide and the most important SCN resistance gene in cultivars is rhg1. This gene has been mapped as a quantitative trait locus (QTL) onto soybean linkage group (LG) G. Our objective was to determine whether the SCN resistance sources PI 437654, Peking, and PI 88788 have different alleles at rhg1 based on resistance phenotypes. Populations segregating for resistance alleles at rhg1 from these sources were screened for resistance to H. glycines in the greenhouse and evaluated with molecular markers linked to rhg1. In the comparison of rhg1 alleles from PI 437654 and PI 88788 with SCN isolate TN14 (HG type 1.2.5.7), plants with the PI 437654 allele had significantly (P < 0.0001) less SCN reproduction than plants carrying the PI 88788 allele. In tests with SCN isolate PA3 (HG type 7), alleles of rhg1 from both sources gave a resistant reaction, although plants homozygous for the PI 88788 allele had significantly (P < 0.05) greater resistance than plants with the PI 437654 allele. In the comparison of PI 437654 and Peking alleles with the SCN isolate TN13, no significant association between markers linked to rhg1 and SCN resistance was observed. These results suggest that PI 437654 and PI 88788 each have a different functional SCN resistance allele at or close to rhg1, however no allelic differences were detected between PI 437654 and Peking. These allelic differences have implications that breeders should consider before incorporation into cultivars.