Yellow rust is the major wheat disease in central West Asia and North Africa. Recently, severe epidemics have occurred, with major yield losses in 2010–2011 in Lebanon and Syria. We conducted an extensive field survey, with a collection of 273 samples of Puccinia striiformis f. sp. tritici , to explore the origin of these epidemics. All samples were genotyped with 20 microsatellite markers, and 54 isolates were pathotyped. The population was dominated by the PstS2 lineage, which has spread worldwide since 2000 and displays considerable pathotype diversity (10 pathotypes). The 22 multilocus genotypes (MLGs) detected corresponded to variants of the clonal lineage PstS2, but they differed from the common PstS2 genotype found in the worldwide study conducted between 1981 and 2010. No strong differentiation was observed between Lebanon and Syria. The dominant MLG in Syria was common to both countries. Nine MLGs were found exclusively in the Syrian population and four were restricted to the Lebanese population, including the dominant MLG in Lebanon. The predominant MLG‐11 was found in nine pathotypes, at high frequency. The dominant pathotype in Syria was virulent against widely deployed resistance genes (Yr2 , Yr6 , Yr7 , Yr9 , Yr25 , and Yr27 ); virulence against Yr3 , Yr8 , Yr17 , and YrSP occurred at various frequencies, but Yr1 , Yr4 , Yr5 , Yr10 , Yr15 , and Yr32 were effective against all isolates. No host effect was detected. The presence of diverse host populations consisting of landraces and elite varieties, and diverse climatic conditions may account for the unexpectedly high diversity of this clonal population.