We report the use of bulked segregant SSR analysis for rapid identification of DNA markers linked to the Fr1 locus in soybean. Pooled DNA extracts from 10 homozygous Fr1 Fr1 and 10 fr1 fr1 F2 plants, derived from a msMOS x Minsoy cross, were analyzed using 65 SSR markers. Five SSRs produced repeatable polymorphisms between paired bulks. Linkage with the Fr1 locus was tested using these five SSR primers and DNA from individual plants of each bulk. DNA polymorphisms generated by these five primers were linked to the Fr1 locus. Linkage of SSR loci with the Fr1locus was verified by using an F2 population segregating for Fr1. The five SSR markers and Fr1 are on linkage group K of the USDA ARS/ISU molecular genetic map. The markers flanking Fr1 are Satt337 (11.0 cM) and Satt044 (0.6 cM). Fr1 previously was mapped on linkage group 12 of the classical genetic map. Thus classical genetic linkage group 12 has been correlated to linkage group K of the molecular genetic map. Six SSR markers were chosen on linkage group K to test the segregation ratio. All six SSRs tested were skewed toward the Minsoy genotype, one chi-square value was statistically significant. This suggested that a gametophyte factor may lie in the region close to Fr1 and most likely close to Satt046.