Allium oreophilum, hitherto the representative of the monotypic A. subg. Porphyroprason from the second evolutionary lineage of Allium, is studied in detail. Over about 150 years, A. oreophilum was regarded as a somewhat polymorphous species with two synonyms, all described in the 19th century. A detailed molecular analysis (ITS and three chloroplast DNA regions: trnQ-rps16 and trnL-trnF intergenic spacers, rps16 intron) of altogether 33 living samples and herbarium specimens showed, however, that the previously described species A. oreophilum, A. ostrowskianum and A. platystemon must be considered good species, and two additional taxa must be newly described. All these taxa are morphologically compared, and an identification key is provided. Three species were karyologically investigated, possessing 2n = 16 chromosomes but showing different karyotypes. A dated phylogeny based on the ITS mutation rate revealed that A. subg. Porphyroprason and subg. Vvedenskya diversified into two sister groups around 21.52 million years ago, in the early Miocene. The possible biogeographic scenario of the origin of A. subg. Porphyroprason, subg. Vvedenskya and other subgenera is presented. A morphological comparison of specimens available from different cultures showed an astonishing variation of characters, and other unidentified taxa of this subgenus likely exist in nature.