Abstract:The molecular phylogeny of the genus Allium which includes eighteen species selected from nine sections was investigated through PCR-RFLP analysis of two chloroplast DNA fragments, including trak gene (approximately 2 520 bp) and rpL16 gene (approximately 1 230 bp). Digestion of these two fragments by 26 restriction endonucleases yielded 303 polymorphic recognition sites, of which 163 were informative sites. The restriction site data matrix were analyzed following the parsimonious Wagner and parsimonious Dollo principle of PAUP ( version 3.1.1 ). Topologically, the most parsimonious Wagner tree constructed by branch-and-bound and heuristic search was similar to the most parsimonious Dollo tree. All the taxa of Allium form a monophyletic group, and five sections based on morphological characters were supported strongly by this result. Sect. Augninum is closely related to Sect. Bromatorrhiza, Sect. Molium is closely related to Sect. Caloscordum. Their reliability was farther confirmed by the bootstrap test very well. In morphology, A. pallasii is closely related to A. caeruleum and belongs to Sect. Haplostemen, A. cepa is closely related to A. galanthum and belongs to Sect. Cepa. But evidence from cladistics of parsimonious tree based on 163 informative sites of PCR-RFLPs showed that they are neither confined to a monophyletic group nor to a natural taxon.