The wheat DREB2 homolog, WDREB2, encodes an EREBP/AP2-type transcription factor that activates downstream Cor/Lea genes and plays important roles in abiotic stress responses. WDREB2 expression is posttranscriptionally regulated by alternative splicing. In this study, the alternative splicing patterns of WDREB2 transcripts were compared among wheats of different ploidy levels. In diploid progenitors, alternative splicing rapidly produced functional forms from the WDREB2 transcripts and the levels of the nonfunctional form gradually decreased in response to drought stress; however, in hexaploid wheat lines, including both cultivars and synthetic lines, the nonfunctional form failed to decrease. The accumulation levels of the three spliced forms in synthetic allopolyploids were not equal to the sum of those in the parental lines. These results indicated that allopolyploidization during wheat polyploid evolution inhibited efficient alternative splicing of WDREB2 transcripts.