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Sexual reproduction is considered indispensable for the long-term survival of a species, as it enables efficient selection against deleterious mutations. Transitions to asexual reproduction happen frequently in eukaryotes, but usually lead to quick extinction of the involved species, attributed to rapid accrual of harmful mutations. Therefore, obligate asexuality is often regarded as an evolutionary dead end. However the mere existence of ancient asexual lineages challenges this point of view. Bdelloid rotifers are a large group of putative ancient asexuals that presumably abandoned sexual reproduction tens of millions of years ago. To address the possibility of recombination in the bdelloid rotifer Adineta vaga on a whole-genome scale, we sequenced genomes of 11 A. vaga clonal lineages. Using several types of analysis we show that the observed patterns of population structure in A. vaga are incompatible with obligate asexuality, thus providing compelling evidence of genetic exchange in this 'ancient asexual' species.