Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships in the common leek (A. ampeloprasum) based on selected samples of this species and its putative relatives in sect. Allium from Iran. The silica-dried leaf samples of 56 accessions representing 23 species of Allium were sequenced for this study, 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL-F were generated and several accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differs slightly in the nuclear versus plastid datasets. In the nrITS tree A. ampeloprasum is retrieved in a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non-concerted copies of nrITS. Close relationships are suggested between following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum, and A. abbasii with A. phanerantherum.