Mapping and cloning of complex quantitative trait loci remain a great challenge in complex highly repetitive genomes such as the grass tribe, Triticeae. This limitation is based upon the availability of markers and frequency of genetic recombination. Most markers are gene-based derived from polymorphisms within genic space. Non-gene-based markers, such as repeat junction markers, are derived from the non-coding intergenic space. Repeat junction markers take advantage of the repetitive nature of the wheat genome, providing random and equal distribution of these markers throughout a chromosome and can facilitate mapping efforts. Repeat junction markers are designed upon the junction of nested repetitive elements and approximately 90% of these markers have been determined to behave as single copy and genome specific. Repeat junction markers were designed from 454 genome sequence of the wheat D-genome progenitor, Aegilops taushcii. Mapping of A. taushcii repeat junction markers to deletion bins within the D-genome of polyploid wheat will allow for the construction of a physical marker scaffold that will aid in genome sequence completion and future mapping and cloning studies. To design an optimal marker array, we tested hybridization temperature, oligo length, and different statistical analysis methods. Here we present our methods for design and analysis of the Nimblegen comparative genomic hybridization arrays constructed from A. taushcii repeat junction markers.