Rotifers of Class Bdelloidea are common freshwater invertebrates in which, despite much study in the field and the laboratory, males and meiosis are unknown. This apparent lack of sexual reproduction and the ancient origin of the Class have posed a challenge to the generally held view that genetic exchange within a population is essential for long-term evolutionary success. In order to examine natural bdelloid populations for evidence of genetic exchange, we cloned and sequenced pairs of homologous regions at two loci in each of six bdelloid isolates belonging to the same cox-1 mitochondrial clade. Three isolates, collected at separate sites in New England, displayed clear evidence of allele sharing at both loci, indicating that bdelloids do, after all, engage in some form of genetic exchange within populations.