Molecular markers linked to alleles of male sterility facilitate identification of mutations and genes that influence developmental processes. Male sterility in soybean has the potential for producing hybrid seed without the need for hand pollinations. The objective of this study was to determine the genetic map location of the male-sterile ms2, ms3, and ms9 loci by molecular mapping using simple sequence repeat (SSR) markers. Three segregating F₂ families were developed from crosses of the cultivar Minsoy (PI 27890) to three different male-sterile, female-fertile lines which displayed very low out-crossed seed set (ms2), and very high out-crossed seed set (ms3, and ms9), in previous evaluations. Minsoy (MsMs) was used as female parent with Ms3 and Ms9 crosses, and as male parent with the ms2ms2 cross. Two hundred thirty-five SSRs were evaluated. Molecular mapping analysis revealed that ms2 locus was located on linkage group O between SSR markers Sat_190 and Scaa001. The ms3 locus was located on linkage group D1b between SSR markers Satt542 and Satt157. The ms9 locus was located on linkage group N between SSR markers Satt521 and Satt660.