Invasions of nonindigenous species have caused ecological devastation to natural communities worldwide, yet the biological bases for invasiveness remain poorly understood. Our studies of invasive watermilfoil (Myriophyllum) populations revealed widespread polymorphisms in biparentally inherited nuclear ribosomal DNA sequences, which were not detected in populations of native North American species. Subclones of the polymorphic regions revealed the occurrence of distinct sequences matching those acquired from both nonindigenous and native North American species. Molecular data demonstrate clearly that invasive watermilfoil populations in North America have resulted from hybridization between nonindigenous and native species. These observations suggest that invasiveness in these aggressive aquatic weeds may be linked to heterosis maintained by vegetative propagation.