Technical Abstract: The occurrence of epidemics of Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, in U.S. winter wheat (Triticum aestivum L.) during the past two decades has resulted in increased emphasis on development of resistant cultivars. Understanding the effect of focused breeding efforts for FHB resistance on the genetic diversity, population structure (PS) and linkage disequilibrium (LD) in soft winter wheat germplasm in the eastern United States is important for marker-assisted breeding and use of association analysis to map resistance QTL. A set of 251 lines selected from three collaborative FHB screening nurseries was genotyped with SSR, STS and DArT markers to assess genetic diversity, PS, and LD,. The genome–wide average of LD decay to r2 < 0.2 was 9.9 cM and moderate levels of LD (r2 >0.2) were generally constrained to markers less than 5 cM apart. Although the lines evaluated were targeted to distinct production zones (northern vs. southern) of the eastern winter wheat region, cluster and principal component analyses did not detect separation of lines into sub-populations. The lack of major sub-groups in these germplasm may be the result of a short, intense breeding history for scab resistance and wide-spread use of common resistant parents. Our data indicated that admixture and sharing of germplasm among U.S. winter wheat programs focused on development of FHB resistant cultivars is common.