Biotic stresses including diseases [leaf, stem and stripe rusts, and wheat streak mosaic virus (WSMV)] and insects [greenbug (GB), Hessian fly (Hf), Russian wheat aphid (RWA) and wheat curl mite (WCM)] significantly affect grain yield and end-use quality of hard winter wheat (HWW, Triticum aestivum L.) in the U.S. Great Plains.  Many genes or quantitative traits loci (QTL) have been identified for seedling or adult plant resistance to these stresses.  Molecular markers for these genes or QTL have been identified using mapping or cloning. This study summarizes the markers associated with various genes including genes or QTL conferring resistances to insects, such as GB (7), RWA (4), Hf (9), and WCM (4) and diseases including leaf, stem and stripe rusts (26) and WSMV (2); genes or QTL for end-use quality traits such as high (3) and low (13) molecular weight glutenin subunits, gliadin (3), polyphenol oxidase (2), granule-bound starch synthase (3), puroindoline (2), and pre-harvesting sprouting (1); genes on rye translocations with 1AL and 1BL; and genes associated with plant height (12) and photoperiod sensitivity (1).  A subset of the markers was validated using a set of diverse wheat lines developed by breeding programs in the Great Plains.  These analyses showed that most markers are diagnostic in only limited genetic backgrounds.  However, some markers developed from the gene sequences or alien fragments are highly diagnostic across various backgrounds, such as Rht-B1, Rht-D1, Ppd-D1, Glu-D1, Glu-A1, and 1AL.1RS.  Knowledge of both genotype and phenotype of advanced breeding lines could help breeders to select right parents to integrate various genes into new cultivars and increase the efficiency of wheat breeding.