Triticale, an intergeneric hybrid crop-plant, is generated when female wheat lines are fertilised with pollen from rye. We have investigated the mitochondrial DNA organisation and the expression of a total of 11 different triticale genotypes, varying in their nuclear and cytoplasmic backgrounds. In Southern hybridisations using probes homologous to the upstream flanking sequences, mtDNA fragments characteristic of both wheat and rye mtDNA can be detected in all triticale lines analysed. In addition, clones isolated fom a triticale lambda library exhibit either a maternal-like or paternal-like organisation of the orf25 gene region. By PCR cloning, four different orf25 gene copies were identified in triticale, three of which correspond to maternal (85%) or paternal (12%) orf25 sequences. Three percent of all clones represent a novel type, that might have arisen by homologous recombination. Although these data suggest biparental inheritance of mtDNA in wheat/rye crosses, paternal-like gene copies can also be detected in maternal wheat mitochondria. Their stoichiometry as assayed by competitive PCR is about 0.1% of total orf25 gene copies. The high abundance of paternal-like sequences in the F1 hybrid might therefore be due to either the transmission of rye mtDNA in the intergeneric cross and/or the amplification of sequences in triticale that persist in sub-stoichiometric amounts in wheat. These data suggest that amplification and recombination of sub-genomic mitochondrial molecules are affected by different nuclear genotypes. Interestingly, sequence analysis of triticale RT-PCR clones indicates a selective transcription of maternal-like orf25 gene copies in triticale. Mitochondrial gene expression may therefore possess mechanisms to compensate for the variation of mtDNA organisation.