Inheritance of mitochondrial DNA in animals is thought to be both strictly maternal and non-recombining. Nevertheless, in the last decade evidence for recombination of mitochondrial DNA has been observed in several animal species, but few reports come from natural populations and most of the time the frequency of individuals possessing more than one mtDNA type is very low. This talk presents evidence for extensive heteroplasmy and mitochondrial recombination in a region of secondary contact of a lizard species (Lacerta lepida). Individuals at the centre of the contact zone possess heteroplasmic point mutations at the mtDNA cytochrome b gene. The heteroplasmic condition was further tested by cloning 20 individuals at the centre of the zone and sequencing 8 to 10 clones per individual. All individuals tested had recombinant mtDNA sequences, often more than one. The results suggest that mtDNA recombination was derived from the fusion of the maternal and paternal mtDNAs due to paternal leakage, which is thought to be more frequent in hybrid zones. To our knowledge this is the first study reporting such extensive heteroplasmy and recombination in the mtDNA genome in natural populations of a species with typical maternal mtDNA inheritance. Our findings suggest that mtDNA may recombine regularly and that secondary contact zones, where highly divergent molecules come into contact, may provide natural laboratories for studying this phenomenon.