Molecular analysis revealed that out of 70 SSR primer pairs (including 40 Yr specific primers) used, 18 SSRs gave amplification. Seven Yr specific markers (Xgwm130 (Yr7), Xbarc 352 (Yr18), Xgwm 11 (Yr26), Xwmc 44 (Yr29), Xwmc 149 (Yr53), WKS1_I (Yr36) and Xcfb309 (Yr47) were polymorphic on RILs population. The amplified products varied from 120 bp to 350 bp. Cluster analysis at molecular level revealed that cluster I was the largest consisting of 39 RILs. This was followed by cluster X (33 RILs), cluster V (2 8 RILs), cluster VII (19 RILs), cluster IX (19 RILs), cluster VI (18 RILs) and cluster XI (18 RILs), cluster XII (15 RILs), cluster VIII (11 RILs), cluster III (7 RILs) and cluster XIII (5RILs). The scattered diagram on the molecular marker diversity analysis revealed that the fourteen RILs (50, 52, 56, 58, 59, 72, 97, 98, 118, 119, 120, 159, 184 and 193) were diverse. The grouping of recombinant inbred lines was not similar as in case of grouping based on morphological traits. Molecular Clustering as well as NTSYS-PC analysis clearly indicated that the recombinant inbred lines were scattered between the two parental wheat genotypes, WH711 and WH542, with an inclination towards WH542 (yellow rust resistant parent).