We present a modification of the representative difference analysis (RDA) technique used to target AT-rich repeated sequences, such as transposable elements, with a double-probe verification system. RDA is a subtractive/amplification PCR-based technology used to identify specific sequences that are different between 2 related genomes.Vsp I restriction enzyme was used to target AT-rich sequences. RDA products were cloned with a high efficiency. Double-probe verification is based on reverse dot-blot of cloned RDA products and uses a positive and a negative probe. We tested thisVsp I-modified RDA on different combinations of bread wheat (Triticum aestivum) and relatives.Triticeae members have large, complex genomes with various ploidy levels. RDA experiments were performed with single or bulked DNA. Reverse dot-blot double-probe verification detected specific repeated sequences quickly and efficiently. Together, the 2 systems provide a powerful tool for obtaining specific transposable elements and repeated sequences that are different between related genomes, regardless of genome size and ploidy.