Soybean has a morphological type with a broadened and flattened stem. Fasciation has been suggested as a new gene for soybean research. SSR marker linked to the ~Large f locus that controls fasciation phenotype has not identified within 10 cM. A mapping population consisting of 94 F2 progenies was derived from a cross between wild type Clark (FF) and fasciation mutant C32 (~Large f~Large f ). The phenotype of F2 individual plants was recorded at R2 and R3 growth stage from field. One-thousand 10-mer oligonucleotide RAPD primers and 29 SSR primers selected from the D1b+W of the soybean molecular linkage map were used. A genetic map was constructed from the segregating 35 RAPD, four SSR markers and one phenotypic(wild type/fasciation) marker. The segregation ratios of 3 : 1 observed in the F2 population and the Chi-square values strongly suggest that the fasciation trait is controlled by a single recessive gene. Satt537 marker was linked to ~Large f locus at a distance of 9.6 cM. Assignment of the ~Large f locus to linkage group D1b+W and identification of markers can be used as an initial step for fine mapping of the ~Large f gene.