Wheat (Triticum aestivum L.) is one of the most important staple food crop worldwide. As a polyploid plant, its origin, evolution and domestication have always been the hotspots of research. Common wheat contains three subgenomes (A, B, and D), the diploid progenitors of the A and D subgenomes have been unequivocally identified. However, due to the extinction of the B parent and the most likely direct maternal progenitor (AABB) for common wheat (AABBDD) has still unclear, which remains a great challenge on the origin study of the subB and subAB subgenomes of common wheat in the field of wheat genetic evolution. Here, we try to solve this particular problem with the specificity of a novel gene family in wheat and by using large population of rare germplasm resources. We identified a novel non-typical CAF1 subfamily without DEDD (Asp-Glu-Asp-Asp) domain, TaCAF1Ia, whose members were extensively duplicated in wheat genome. The replication events had started and constantly evolved from ancestor species. Specifically, it was found that a key member TaCAF1Ia1 was highly specialized and only existed in the subB genome and the S genome. Unlike CAF1s reported in other plants, the TaCAF1Ia1 genes may be new factors for anther development. These atypical TaCAF1s could also form CCR4-NOT complex in wheat but with new interaction sites. Utilizing the particular but conserved characters of the TaCAF1Ia1 gene, the comparative analysis of haplotypes composition for TaCAF1Ia1 were identified among wheat populations with different ploidy levels. Based on this, the dual-lineages origin model of the maternal progenitor for common wheat and potential three lineages domestication model for cultivated tetraploid wheat were proposed. This study brings fresh insights for revealing the origin of maternal progenitor for common wheat and the function of CAF1 in plants.