Identification and exploitation of useful and novel alleles at quantitative trait loci (QTL) within germplasm is crucial for successfully improving malting barley. Improvements in agronomic traits have always been a challenge to breeders, because stringent requirements set by maltsters and brewers greatly influence new cultivar development. We investigated the marker trait associations for plant height and grain yield QTL over the entire genome in a collection of 768 breeding lines from University of Minnesota and North Dakota State University barley improvement programs. The agronomic data were obtained from the Barley Coordinated Agricultural Project trials over 4 years (2006, 2007, 2008 and 2009) grown at several locations in Minnesota and North Dakota, USA. We used 3,072 single nucleotide polymorphisms to detect trait-marker associations. We used principal component analysis to determine sub population grouping, identity-by-state genotypic similarity matrix to determine fine scale relationship between lines, and mixed-linear model (MLM) for association analyses. Our preliminary results suggests that: 1) the first two principle components defined two subpopulations corresponding to the two breeding programs, 2) adjacent markers are in strong linkage disequilibrium (LD) with each other, but LD decayed within 10 cM, 3) association mapping could be used for identifying QTL from breeding lines, 4) markers associated with plant height and grain yield were different between MN and ND breeding programs, 5) analyzing lines from individual breeding programs separately will help barley breeders to focus on QTL relevant to their breeding program and target environment; however, combining data sets can increase power to detect QTL.