Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, skip meiosis therefore their chromosomes do not undergo recombination. Fast phenotypic responses of apomicts to selection on short time scales indicate that apomixis imposes immediate reproductive isolation on the polyploid lineages, interferes with genetic cohesion forming fragmented gene pools into populations that develop independently, increases expansion range and ecological plasticity. Despite the progress in the study of apomixis, molecular genetic regulation of the latter remains poorly understood. This article presents in silico characteristic of the apomixis associated genes CENH3 and APOLLO. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. Disruption of meiosis in A. thaliana CENH3 mutants resembles the major components of apomictic reproduction leading to apomeiosis. In this study, we characterized the structure of the CENH3 and its expression levels in flower buds of the natural diploid apomictic and sexual Boechera species at the stage of around fertilization. After the fertilization CENH3 expression decreased in apomictic flower buds and increased in sexual ones. These results might indicate to a role of CENH3 in apomictic development in Boechera species. While CENH3 was a single copy gene in all Boechera species, the APOLLO (Aspartate Glutamate Aspartate Aspartate histidine exonuclease) gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. We also discuss polymorphism and phylogeny of APOLLO and CENH3 genes.