A newly identified genie male-sterile mutant in soybean [Glycine max (L.) Merr.] has high seed set under natural field conditions and is potentially useful in breeding programs. Meiosis is normal in the mutant line. Sterility in this mutant is caused by failure of cailose dissolution at the tetrad stage, which results in microspore abortion; however, little is known about the male-sterile gene at the molecular level. The objective of this study was to identify molecular markers linked with the male-sterile gene (ms) and to place the ms gene onto the soybean molecular genetic map. An F2 population of 107 individuals was constructed from a cross between the mutant msMOS (ms ms) and the cultivar Minsoy (Ms Ms). Two hundred seventy markers, including 219 RFLP and 51 SSRs, were evaluated. Of these, 102 RFLP probes and 31 SSR markers detected polymorphisms between the parents. The F2 population was screened for segregation of these polymorphic molecular markers. Analyses revealed that the male-sterile locus, designated ‘ms’, was located on linkage group D1b of the USDA/ISU soybean molecular genetic map. The availability of linked DNA markers will facilitate the genetic analysis of this male-sterility gene in relation to soybean breeding programs, and will be a starting point for the isolation of the ms gene by map-based cloning.