The absence of chromosome 7D in the wheat–Thinopyrum ponticum partial amphiploid BE-1 was detected previously by multicolour genomic in situ hybridization, sequential FISH (fluorescence in situ hybridization) using repetitive DNA probes, and SSR marker analysis. In the present study the previous cytogenetic and SSR marker analyses were expanded to include 25 other SSR markers assigned to wheat chromosomes 7A and 7D to confirm the presence of a 7A.7D translocation and to specify its composition. An almost complete chromosome 7A and a short chromosome segment derived from the terminal region of 7DL were detected, confirming the presence of a terminal translocation involving the distal regions of 7AL and 7DL. In both cases the position of the translocation breakpoint was different from that of known deletion lines. The identification of the 7AL.7DL translocation and its breakpoint position provides a new physical landmark for future physical mapping studies, opening up the possibility of more precise localization of genes or molecular markers within the terminal regions of 7DL and 7AL.