Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rustdisease and breakdown of major resistance genes in wheat. We conducted a genome wide associationstudy on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. Highlevel of disease variation was observed among locations and a core-set of germplasm showed consis-tence performance. Linkage disequilibrium (LD) decayed rapidly (R2≈ 0.16 at 0 cM) due to germplasmpeerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across allenvironments representing five QTL. The extensively short LD blocks required us to repeat the analysiswith less diverse subset of 220 landraces in which R2decayed below 0.2 at 0.3 cM. The subset GWASresulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detectedin the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical originof this germplasm through time have permitted for selecting novel resistance loci.