DNA markers are powerful tools for verifying the varietal identity and genetic homogeneity of F₁ hybrid seeds. F₁ varieties are becoming increasingly prevalent in bunching onion (Allium fistulosum L.) production in Japan because of the high uniformity of agronomic traits. However, bunching onion is an allogamous crop and suffers from severe inbreeding depression when selfed. It is considered that not only open-pollinated varieties but also the parental lines of F₁ hybrids should maintain a certain degree of average heterozygosity and hence genetic heterogeneity. In the present study, the genetic homogeneity of eight bunching onion varieties, including six F₁ hybrids, was evaluated using 14 SSR markers. Two or more polymorphic alleles were detected at all of the SSR loci examined in each variety. The number of alleles detected in the eight varieties ranged from 3 to 7 among the 14 SSR loci, and the polymorphism information content from 0.41 to 0.76. All the varieties examined displayed very low degrees of uniformity at all of these polymorphic loci. Based on these results, it may be impossible to determine an appropriate genotypic identity for any of the existing bunching onion varieties. To facilitate and enhance the accuracy of variety identification, we proposed here an “SSR-tagged breeding” scheme in which the plants homozygous at a few SSR loci would be selected out of a foundation seed field. This scheme may enable to achieve efficient variety identification and purity determination of F₁ seeds not only in bunching onion but also in any allogamous crops exhibiting severe inbreeding depression.