The distribution of highly repetitive DNA sequences on chromosomes of tetraploid and hexaploid cytotypes of Aegilops crassa (Dcr1Xcr and Dcr1XcrDcr2 genomes) was studied using C-banding and in situ hybridization analyses with the pSc119, pAs1 and pTa794 DNA clones. In total, 14 tetraploid and five hexaploid accessions were examined. All chromosomes can be identified by their C-banding and ISH pattern with the pAs1 DNA clone. Only a few pSc119 hybridization sites were observed in the telomeric regions of several chromosomes. We found a high level of C-banding polymorphism and only minor variations in labeling patterns. The position of C-bands generally coincided with the location of the pAs1 sequence. Three 5S rDNA loci were detected in tetraploid Ae. crassa, whereas five pTa794 ISH sites were observed in 6x Ae. crassa. All the hexaploid accessions differed from the tetraploids by a reciprocal non-centromeric translocation involving chromosomes A and N. Three additional translocations were detected in the accessions analyzed. The Dcr1 genome of 4x Ae. crassa is highly modified compared with the D genome of the progenitor species Ae. tauschii. Because of the large amount of chromosomal rearrangements, the origin of the Xcr genome remains unknown. The second Dcr2 genome of 6x Ae. crassa is different from the Dcr1 genome but is similar to the D-genome chromosomes of Ae. tauschii, indicating that no additional large rearrangements occurred at the hexaploid level.