ISSR amplification was evaluated for its applicability to onions identification. The procedure was tested on six onions including: Allium cepa L. (onion), Allium tuberosum Rottl. ex Spreng. (chinese chives), Allium ascalonicum L. (shallot), Allium cepa L. var. proliferum (top onion), Welsh onion (Allium fistulosum L.) and Welsh onion ‘Sprint’. Thirty primers homologous to microsatellite repeats based on various di-, tetra- and penta- SSR motifs with 3’ selective nucleotides for anchoring, were screened against the onion genome by 2% agarose gel electrophoresis. Out of the 30 primers 16 gave stable patterns amplifying a total of 187 loci of which 159 (85%) were polymorphic. Clearly detectable ISSR amplicons ranged from 139 to 2213 bp in size. The average number of loci gene-rated per primer was 12. Specific ISSR loci were detected for each onion species. The highest number (15) of species-specific loci were obtained for A. tuberosum, whereas the lowest number (3) was detected for A. ascalonicum. UPGMA cluster analysis was used to construct a dendrogram and to estimate the genetic distances between the Allium species. The tree revealed one separate group including A. fistulosum ‘Sprint‘, A. cepa var. proliferum, A. fistulosum and A. ascalonicum. In this group the smallest divergence is observed between A. fistulosum ‘Sprint‘ and A. cepa var. proliferum (77.9% similarity). The two other species: A. cepa and A. tuberosum are approximately equidistant from the group.

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