Technical Abstract: In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17,000Mb), repeat DNA accounts for ~ 90% of the genome of which transposable elements (TEs) constitute 60-80 %. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs between the homologous wheat genomes are conserved and collinear based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Ae. tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shot gun sequences were used to search for RJM. Out of the 300 RJM primer pairs tested, 269 (90 %) amplified single bands from diploid Ae. tauschii wheat. Of these 269 primers pairs, 260 (97 %) amplified in hexaploid wheat and 3 % amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88 % were successfully assigned to individual chromosomes of the hexaploid D genome. Among the thirty eight RJM primers mapped on chromosome 6D, 31 (82 %) were unambiguously mapped to delineated bins of the chromosome 6D using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome. ----------------------------------------------------------------------------