A total of 12 polymerase chain reaction (PCR) primer pairs were used in genetic studies of wild Allium species (A. grayi R.) and its allied species (A. vineale). Those primer pairs derived from A. cepa and A. fistulosum revealed a lot of polymorphic amplicons among A. grayi collected from 36 different areas and A. vineale collected from 2 areas. 80 microsatellite markers were used for interspecific taxonomic analyses among those species. The data support the results obtained recently from performed karyotype and phylogeography analyses, suggesting the potential of microsatellite markers for use in evaluating the genetic relationship in A. grayi species. Direct sequencing of single amplicons derived from ACE008, ACE057, AFC03G02 was performed, showing the microsatellite motifs were contained in the amplified productions.