Wild emmer wheat (Triticum turgidum ssp. dicoccoides, BBAA), the wild progenitor of cultivated tetraploid and hexaploid wheats, provides an important reference for investigating centromere reorganization during polyploidization and domestication. Here we generated a near-complete genome assembly of wild emmer wheat, including centromeric regions for all 14 centromeres. Comparative analyses with cultivated tetraploid and hexaploid wheats revealed extensive variation in centromere-associated sequences and centromere-proximal structure, as well as distinct subgenome-associated patterns in the A and B subgenomes. The A subgenome was characterized by positional shifts and sequence turnover of CRW-rich centromere-derived blocks, whereas the B subgenome showed reduced CentT566 satellite abundance accompanied by localized retention or expansion on specific chromosomes. These results provide a high-resolution tetraploid wheat reference and reveal subgenome-associated patterns of centromere remodeling during wheat polyploid evolution.