Technical Abstract: Nuclear restriction fragment length polymorphisms (RFLPs) were used to estimate relationships among 14 elite commercial inbreds of bulb onion (Allium cepa) from Holland, Japan, and the USA. Variability for known alleles at 75 RFLP loci and 194 polymorphic fragments revealed by 69 anonymous cDNA probes and a clone of alliinase were scored to yield genetically characterized and uncharacterized data sets, respectively. The inbred onion populations possessed greater than two alleles at 20 of 43 (46%) codominant RFLP loci. Relationships among the inbreds were estimated by cluster analysis of simple-matching (genetically characterized data) and Jaccard (genetically uncharacterized data) coefficients using the unweighted-pair-group method and agreed with known pedigrees. RFLPs distinguished confidently among elite inbreds within and between specific market classes. Virtual hybrids generated by combining gametic arrays from inbreds were analyzed as described above. Allelic and random RFLPs distinguished confidently among hybrids of the same market class, even though heterozygosity for many markers produced a majority of monomorphic fragments. Calculating simple-matching and Jaccard distances, noting the numbers of probes that were unable to distinguish any two inbreds or hybrids. As few as 10 polymorphic probe enzyme combinations distinguished among any two inbreds and 20 mapped or 10 anonymous clones distinguished any two of the virtual hybrids. This study demonstrated that previously reported RFLPs observed among open pollinated onions were due to the highly heterozygous nature of OP onion populations.