Stem rust caused by Puccinia graminis Pers.f.sp.tritici Eriks.and E.Henn.(Pgt) is one of the most destructive diseases of wheat which causing considerable yield losses in wheat growing areas worldwide. It has become a renewed threat to global wheat production after the emergence and spread of race TTKSK (also known as Ug99) and related races from Africa. Races of the pathogen in the "Ug99 lineages" are of international concern due to their virulence for widely used stem rust resistance genes and their spread throughout Africa. Disease resistant cultivars provide one of the best means for controlling stem rust. Bale zone, located on the Southeast part of Ethiopia, is one of the main wheat growing regions, playing a pivotal role in the wheat stem rust epidemic in Ethiopia. This study investigated levels of resistance in key wheat cultivars (lines) grown in Bale zone using seedling resistance evaluation and marker aided selection. Twenty wheat cultivars were evaluated for their response to stem rust infection at seedling stage under green house condition. Wheat cultivars were challenged with four stem rust races viz TTKSK, TRTTF, TTTTF and JRQCQ. A high level of phenotypic variation was observed in response to these races in the test entries, allowing for selection in these germplasm as a pre-breeding work. Out of the tested cultivars, three wheat cultivars exhibited low infection types (0-2) response to all the four races and hence selected as a source of resistance to stem rust. In addition, the existence of Sr2, Sr22, Sr24, Sr25, Sr26, Sr35 and Sr36 genes in wheat cultivars were assessed using specific DNA markers. Using molecular markers, resistance gene Sr2 was identified in 2 cultivars and Sr24 in five cultivars. However, no Sr25, Sr26, Sr35 and Sr36 were identified in any cultivars tested using DNA markers. The results of both seedling evaluation and marker based resistance gene identification will enable to breed wheat varieties with durable resistance to stem rust disease.