Saccharomyces offer a unique opportunity to study reproductive isolation and origin of a new species via speciation of interspecific hybrids. Most studies involved only the nuclear genomes, although some hybrids possess recombined mtDNA. To shed the light on mtDNA recombination we constructed S. paradoxus/S. cerevisiae interspecies hybrids from S. cerevisiae strains with variable intron content in mtDNA and characterized their mtDNA. Interspecific hybrids obtain largely recombinant forms of mtDNA triggered by intron transposition where the coconversion of neighboring exons is involved. Either functional hybrids with complete mtDNA or fragmented ρ^- genomes arise that produce petite colonies. Much has been written about the importance of parasitic surplus introns. Our data emphasize their beneficial potential in the case if a "foreign" mtDNA appears in mitochondria. They either provide opportunity to transfer a large part of the original genome in offspring (hybrid mtDNA) or can be "suicidal" and eliminate foreign DNA to petite colonies.