Primers (10-mers) of random sequence were used to amplify RAPD bands from genomic DNA of an F1 strain of flax rust (Melampsora lini) and its two parent strains. One primer out of 160 tested was unusual in that it amplified a product from F1 DNA that was not amplified from either parental DNAs. The same primer also generated two RAPD bands that segregated as codominant alleles amongst F2 progeny. The nonparental band was only generated from DNAs of F2 individuals that were heterozygous for these two allelic sequences. Sequence analysis of the two RAPD alleles demonstrated greater than 99% sequence identity, although the larger allele possessed an additional 38bp relative to the smaller. Mixing of the two allelic sequences followed by denaturation and annealing in the absence of polymerase activity resulted in the formation of the nonparental band. Thus the nonparental band present in some RAPD reactions consisted of a heteroduplex molecule formed between two allelic sequences of different size. These data demonstrate that heteroduplex molecules formed between allelic RAPD products are a potential source of artifactual polymorphism that can arise during RAPD analysis.