Puccinia graminis f. sp. tritici, the causative agent of stem rust in wheat, is known for its high virulence variability and ability to evolve new virulence to resistance genes. Thus, pyramiding of several resistance genes in a single line is the best strategy for a sustainable control of wheat stem rust. Sr13 is one of the few resistance genes that are effective against wide ranging P. graminis f. sp. tritici races, including the pestilent race Ug99. Its effectiveness to Ug99 makes it a valuable source for resistance to stem rust. Molecular markers play a pivotal role in the genetic characterization of the new sources of resistance as well as in stacking two or more resistance genes in a single line. Therefore, the aim of this study was to develop molecular markers for Sr13 facilitating efficient pyramiding of Sr genes. Based on the 158 F(2) individuals derived from a cross of Khapstein/9*LMPG × Morocco and SSR analyses, the Sr13 locus was mapped on chromosome 6A of wheat, and a genetic map comprising about 90 cM was constructed with the closest marker barc37 being located 4.0 cM distally of Sr13. Of the nine mapped markers, barc37 amplified an allele specific for the presence of Sr13 as shown by testing different cultivars and breeding lines. These newly developed markers will increase the efficiency of incorporating Sr13 into cultivars that are widely adopted, but susceptible to hazardous Ug99 and/or assist for the development of new elite lines that are resistant to Ug99.