Allium sect. Codonoprasum represents an evolutionarily young and rapidly radiating group of bulbous geophytes, with a significant proportion of polyploids and minor morphological differences between species. In the last 20 years, dozens of new species of this section have been described from the Mediterranean. Still, very little new information has been obtained on most of them since their description, especially concerning cytogenetic, molecular, and distribution data. Allium goumenissanum is a recently described species of this section, known only from three nearby localities in northern Greece. During the last 10 years, the senior authors' team collected population samples of an unknown species of this section from the southern Balkans, which appeared to be representative of A. goumenissanum. Using an integrated approach employing a range of methods (cytogenic, molecular, morpho- and micromorphological methods), the populations of an unknown species were compared with morphologically similar species A. goumenissanum and A. stamatiadae. AFLP, ITS sequencing and genome size analyses revealed that all the populations of the unknown species represent A. goumenissanum, and that this species is differentiated genetically and in genome size from A. stamatiadae. ITS sequencing indicates an allotriploid origin of A. goumenissanum from unknown ancestors. The characterization of the morphology and reproduction of A. goumenissanum is completed and micromorphological and anatomical characteristics of the leaves of both species are newly published. The distribution of A. goumenissanum, based on new data, now includes a more extensive area of north central Greece and the species has been found as a new one for Bulgaria.