Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is one of the most important diseases of wheat, worldwide. New sources of resistance to stem rust could be found in synthetic hexaploid wheat (SHW) genotypes due to their high genetic diversity. In order to recognize the genetic structure of the population of the stem rust, following race analysis of 12 Pgt isolates, resistance of 348 SHW genotypes were evaluated using the infection type on a scale of 0 to 4 ratio to the four selected isolates from Gorgan and Broujerd (in 2014 and 2015) at seedling stage using randomized complete block design with two replications. Based on the reactions of differential wheat genotypes, the Pgt races TKTTF and TTTTF were identified among all isolates displaying virulence on the stem rust resistance genes Sr5, Sr6, Sr7a, Sr7b, Sr8a, Sr8b, Sr9a, Sr9b, Sr9d, Sr9e, Sr9g, Sr10, Sr12, Sr14, Sr15, Sr16, Sr17, Sr18, Sr19, Sr20, Sr21, Sr22, Sr23, Sr28, Sr30, Sr34, Sr36, Sr37, Sr38, SrTmp and SrMcN. Combined analysis of variance showed statistical significance between SHW genotypes in seedling stage in terms of their reaction to Pgt isolates. Furthermore, the significant isolate × genotype interaction suggests isolate-specific resistance in some genotypes which displays resistance to at least one Pgt isolate. Isolate-specific resistance was observed in 16% of genotypes, whereas 61 and 23% of the SHWs (such as lines 22842, 22857, 22862, 22863, 22864) were susceptible (infection type of 3-4) and resistant (infection type of 0-2) to all four Pgt isolates, respectively. Results of this research as the first report of SHWs resistant to prevalent Iranian stem rust races could be exploited in breeding programs using identified resistant genotypes which carry seedling resistance genes.