Wheat is an allohexaploid (2n=6x=42) that originated after two independent events of polyploidization with three subgenomes that can pair with one another. To maintain the integrity of the nucleus and reduce abnormal meiotic behavior, a precise mechanism to regulate chromosome pairing is required that differentiates not only homologous from nonhomologous chromosomes but also differentiates homoeologous chromosomes for the normal bivalent formation and accurate recombination. Recently, a candidate Ph1 gene (C-Ph1) characterized using reverse genetic tools controlled the diploid-like pairing behavior of wheat. Further, structural differentiation of C-Ph1-5B copy via 29bp deletion or 60bp insertion from its two homoeologs suggested neofunctionalization after polyploidization. Thus, to understand polyploidization induced changes in the evolution of C-Ph1 gene structure and expression, C-Ph1 gene was studied in diploid progenitors of wheat. Comparison of diploid C-Ph1 gene variants with polyploid gene variants revealed that 29bp deletion in C-Ph1-5B copy is polypoid specific. Copy specific expression analysis of C-Ph1 homoeologs in polyploid wheat revealed that meiosis-specific upregulation of gene expression with C-Ph1-5B showing significantly higher transcript abundance compared to its homoeologs. Further comparison of the change in gene transcript abundance with diploid progenitors revealed downregulation of gene expression for C-Ph1-5A and C-Ph1-5D copies, whereas C-Ph1-5B copy showed upregulation after polyploidization. Gene expression analysis for copy-specific transcript abundance in accessions of wild emmer wheat segregating for chromosome pairing revealed significantly lower transcript accumulation for C-Ph15B copy during prophase-I in accessions with higher order chromosome pairing compared to accessions with no higher order chromosome pairing. Thus, suggesting that differential transcript accumulation specifically during early meiosis is critical for Ph1 gene function.