Chromosome elimination of one parental species in hybrid cell observed even after successful fertilization is one of a common phenomenon and the main problems of remote hybridization. Centromeres regulate the process of faithful segregation of chromosomes during cell division. Constant component of the centromeric chromatin is a specialized histone H3 modification (CENH3). CENH3 consists of a conserved C-terminal domain (HFD) and a more variable N-terminal tail (NTT), which plays an important role for CENH3 loading in centromeric chromatin during cell division. In the present study, we performed comparative analysis of CENH3 variants expression in allopolyploids, as well as in different parental varieties of rye (Secale cereale L.) and wheat (Triticum aestivum L.). The varieties of both genera were used as maternal plants. In the coding sequences of the NTT CENH3 we identified the full-length copies of 216 bp with characteristic single nucleotide polymorphisms (SNPs), and copies with 21 bp or 66 bp deletions. The wheat and rye NTT CENH3 copies with 21 bp deletion have not differences in the nucleotide sequences, the rye copies with 66 bp deletion reveal two specific SNPs, which were also found in plant of wheat-rye allopolyploids having 57 chromosomes. The full-length sequences of rye NTT CENH3 show specific SNPs, which were also detected in the full-length sequences of all analyzed plants of wheat-rye allopolyploids. These results indicate that expression of CENH3 copies belonging to each parent was observed in hybrid genomes of aneuploids which arose from octoploid triticale. The NTT CENH3 copies with deletions were not found in secalotriticum (Secalotriticum). The full-length sequences show two rye specific SNPs. Their frequency in secalotriticum significantly exceeds that in hexaploid triticale Mikhas. This fact points to the preferential synthesis of the full NTT CENH3 copies of the rye parental variety in the secalotriticum genome.