Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), and stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), are economically important diseases of wheat. A new race of Pgt (Ug99) and its variants have overcome widely deployed stem rust resistance genes creating an impending risk to wheat production worldwide. Wheat landraces from diverse geographic regions are a potential source of novel rust resistance genes. Six hundred and fifty-two landrace accessions that originated from 54 countries were screened for resistance to Ug99 at Stem Rust Resistance Screening Nurseries in Njoro, Kenya and for resistance to current races of Pst in Pullman, WA. One hundred and thirty landraces and 99 landraces were identified as having resistance response to Ug99 and to Pst in field, respectively. Fourteen landraces showed resistance response to both Ug99 and Pst. The same 652 landraces were genotyped with microsatellite markers covering the whole wheat genome. Phylogenetic analysis based on microsatellite data grouped the resistant landraces into different clusters in the dendrogram suggesting that resistant genotypes are genetically diverse and are expected to possess different novel resistance genes. Landraces with resistance to stem and stripe rust have both global and regional importance as sources to develop new and diverse resistant germplasm.