Stem rust resistance gene Sr13, found frequently in tetraploid wheats, was tested effective against Puccinia graminis f. sp. tritici pathotype Ug99 (TTKSK) and its derivatives. It remains a candidate for developing new cultivars with diverse combinations of stem rust resistance genes. To combine Sr13 with other genes that produce a similar phenotype, linked markers would be required. We used the AFLP approach to identify markers linked closely with Sr13. The STS marker AFSr13, derived from an AFLP fragment, mapped at 3.4–6.0 cM proximal to Sr13 across three mapping populations. Marker dupw167, previously reported to be linked with Sr13, mapped 2.3–5.7 cM distal to Sr13 in four F₃ populations. Marker gwm427 mapped proximal to AFSr13 in two populations, and these markers were monomorphic on one population each. The map order dupw167–Sr13–AFSr13–gwm427 was deduced from the recombination data. Markers dupw167 and AFSr13 were validated on 21 durum wheat genotypes. Combination of dupw167 and AFSr13 would facilitate marker-assisted selection of Sr13 in segregating populations. At the hexaploid level, only gwm427 showed polymorphism and differentiated the presence of Sr13 in 10 of the 15 backcross derivatives carrying Sr13 from their Sr13-lacking recurrent parents.