The wheat stem rust resistance gene Sr36, derived from Triticum timopheevi, confers a high level of resistance against a new race (TTKS, or commonly known as Ug99) and many other races of Puccinia graminis f. sp. tritici. Because Sr36-virulent races exist, breeding for durable resistance would require pyramiding Sr36 with other genes, a process that can be facilitated by DNA markers. The aim of this study was to identify and validate microsateilite markers for the detection of Sr36 in wheat breeding programs. Two populations of 122 F2 (LMPG x Sr36/9*LMPG) and 112 F2 ('Chinese Spring' x W2691Sr36-1) were evaluated for stem rust reaction. Both populations exhibited distorted segregation with a preferential transmission of the Sr36-carrying segment. Three markers, Xstm773-2, Xgwm319, and Xwmc477, were in complete linkage with Sr36 in the LMPG x Sr36/9*LMPG population. In the Chinese Spring x W2691Sr36-1 population, Xgwm319 was 0.9 cM away from Xstm773-2, Xwmc477, and Sr36. These codominant markers were easy to score and diagnostic for Sr36 in a set of 76 wheat cultivars and breeding lines developed in 12 countries. Together, these markers can be used in marker-assisted selection of Sr36.