The rice DEP1 (DENSE AND ERECT PANICLE1) gene is an important regulator that can enhance meristematic activity, reduce internode distance, increase per spike grain number, and eventually increase the rice yield. We report here the cloning of the genomic sequence of the wheat orthologous gene TaDEP1 which contains five exons and 4 introns. Genomic sequence comparison revealed a region that can be used as molecular marker (Ta956) to distinguish homoeoalleles of hexaploid wheat. Ta956 was used to map TaDEP1 to wheat chromosomes 5A, 5B, and 5D by using Chinese Spring nulli-tetrasomic lines. Sequences corresponding to Ta956 were then isolated and sequenced from hexaploid wheat, its putative donor species and tetraploid wheat. Sequence comparison showed that most variations were present at introns, particularly between the B and D homoeoalleles. Domain analysis showed that proteins from the D genome of hexaploid wheat was more different to those on the A and D genomes, suggesting functional divergence among TaDEP1 proteins from the A, B, and D genomes. The potential of using Ta956 as a marker for variety identification is discussed.