Some interspecific plant hybrids show unequal transmission of chromosomes from parental genomes to the successive generations. We revealed that this is caused by the differential behavior of parental chromosomes during meiosis. In male meiosis of Festuca x Lolium hybrids, Festuca univalents were attached less frequently to microtubules than Lolium univalents, lagged in divisions and formed micronuclei, which were subsequently eliminated. Furthermore, we found that outer kinetochore proteins NDC80 and NNF1 were exclusively expressed from the Lolium allele. We hypothesize that silencing of Festuca alleles results in improper attachment of Festuca chromosomes to karyokinetic spindle and subsequently their gradual elimination.