Eb and Ee genomes of the genus Thinopyrum and R genome of the genus Secale produced a DNA fragment of the same length in PCR using a pair of primers designed from a RAPD marker for the Eb genome. After digestion with certain restriction endonucleases, the STS marker was converted into genome-specific CAPS markers. Previously, the Eb-specific RAPD marker has been shown to be a dispersed repetitive sequence occurring on all seven chromosomes of Thinopyrum bessarabicum. Using disomic addition lines of Triticum aestivum with Th. bessarabicum (Eb), Th. elongatum (Ee), or S. cereale (R) chromosomes, the presence of CAPS markers on individual chromosomes of the three genomes was assayed. Because the STS marker is absent in CS, either the STS marker or the CAPS markers can be used to monitor the introgression of chromosomal segments of these three genomes into CS chromosomes. The CAPS markers are also useful in ascertaining genome constitutions of Triticeae species.