Repetitive DNA sequences are thought to be involved in the formation of chromosomal rearrangements, which are important in polyploid speciation. Molnár et al. analyse the chromosomal distribution of microsatellite clusters in relation to the intergenomic translocations in the allotetraploids Aegilops biuncialis and Ae. geniculata. They find that translocation breakpoints are frequently mapped to SSR-rich chromosomal regions, suggesting that microsatellite sequences may facilitate the formation of chromosomal rearrangements.