Centromeres in eukaryotic species are defined by the presence of a centromere-specific histone H3 variant, CENH3. CENH3 plays a key role in recruiting other centromeric proteins; thus, it is the central component in kinetochore formation and centromere function. The CENH3 proteins in several plant and animal species were found to be under positive selection, which was hypothesized to respond to the rapid changing of the repetitive DNA sequences associated with the centromeres. Here, we report the expression and evolution of the CenH3 genes in two allotetraploid rice species as well as their representative diploid progenitor species. Both copies of the CenH3 genes were transcribed in the two allotetraploid species and showed a nonpreferential expression pattern. Contrasting positive and stabilizing selection of the CenH3 genes was associated with different diploid Oryza species. This lineage-specific adaptive evolution of CENH3 was maintained in the two allotetraploid species. Thus, we demonstrate that the allopolyploidization events did not alter the expression or evolutionary patterns of the CenH3 genes in the Oryza species.