The major gene Q/q, an important gene for wheat domestication, is a member of the AP2 (APETALA2)class of transcript factors, named as WAP2. In the present study, we firstly isolated the WtAP2 allele on 5D from Aegilops tauschii Coss., the D-genome donor species of common wheat. The WtAP2 shared with AP2 gene from Arabidopsis in the central core of the AP2 polypeptide, highly basic 10-amino acid domain and AASSGF box, although there were lots of differences in the 37-amino acid serine-rich acidic domain and the remaindering regions. WtAP2 was highly homologous to those of homoeologous loci on 5A and 5B of wheat both on nucleotide and amino acid level. However, there were some variations probably related to gene function. In the first AP2 domain,the amino acids VYL on 5D and 5A loci were replaced with LLR on 5B. In the 37-amino acid serine-rich acidic domain,WtAP2 on 5D had extra amino acid insertion. There was also variation at the position 329 amino acid that was thought to be related with the appearance of free-threshing wheat. At this position, the amino acid is isoleucine on 5Afor Q allele and valine for q allele, while the amino acid is leucine on 5D and 5B. Furthermore, aStowaway MITE insertion was present in the ninth intron of WAP2 on 5B of all common wheats and partial tetraploid Triticum turgidum wheats. These results provided new clues for the studies on the evolutionary biology of WAP2 and origin of common wheat.