The genus Allium L comprises over 1000 species with important nutritional, medicinal and horticultural applications. The natural flora of Kazakhstan is rich in Allium species, including the wild long-pointed onion, A. longicuspis and cultivated A. sativum garlic varieties. It has been hypothesized that A. longicupis is ancestral to A. sativum. We investigated genetic polymorphism in samples of A. longicupis and the A. sativum cultivars "Niki" and "Merey" using start codon targeted polymorphism analysis. Nuclear ribosomal DNA fragments were purified, amplified and tested with 25 primers, finally selecting 12 primers that identified polymorphisms. DNA samples were sequenced, electrophoresed and cluster analysis performed by the construction of dendrograms and principal component analysis. The karyotypes of the different samples were also compared. The results showed that the samples of A. longicupis from natural populations did not differ significantly from those of the cultivated garlic varieties. The results indicate that A. longicupis can be considered a feral, rather than an ancestral, form of A. sativum. These findings have implications both for the breeding and cultivation of garlic varieties and for the taxonomy of the Allium genus.