Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent-of-origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid, tetraploid, and hexaploid wheat via high-throughput transcriptome sequencing at various stages of development. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52.7% of which exhibited dynamic expression patterns at different developmental stages. Gene ontology enrichment analysis suggested that MEGs and PEGs were involved in metabolic processes and DNA-dependent transcription, respectively. Of the imprinted genes, 51.4% exhibited conserved expression patterns during wheat hexaploidization. Forty percent of the homeolog pairs originating from whole genome duplication were consistently maternally or paternally biased in the different subgenomes of hexaploid wheat. Furthermore, imprinted expression was found for 41.2% and 50.0% of homolog pairs that evolved by tandem duplication after genome duplication in tetraploid and hexaploid wheat, respectively. In addition, the timing of endosperm cellularization and accumulation of starch granules differed between reciprocal crosses of tetraploid and hexaploid. We also found that interploidy compared to intraploidy cross affects genomic imprinting for genes in AA and BB subgenomes, with 28.4% (27/95) of imprinted genes showing altered parental allele expression patterns. In addition, hexaploid intraploidy crosses between CB037 inbred line and lines that differ only for distinct DD subgenome origin (TAA10 and XX329) also influence imprinting. These findings indicate that, in wheat endosperm, subgenome interplay reprograms imprinting at genome-wide level, possibly due to modified parental allele expression ratio and gene expression level.