A revision of the Allium species of the section Molium in the Canary Islands is presented. As part of the phylogenetic revision of the Eurasian representatives of the subgenus Amerallium we found large disagreements in the nomenclature and taxonomy of Allium roseum in the floristic publications on the flora of the Canary Islands. At least four species of the section Molium are mentioned for the flora of the Canary Islands: Allium roseum, A. subvillosum, A. subhirsutum and A. trifoliatum. To learn more about the phylogenetic relationships within a group of closely related species of the section Molium, we used maximum parsimony and Bayesian analyses of combined nuclear (ITS—internal transcribed and ETS—external transcribed spacers of rRNA genes) and three chloroplast (rpl32-trnL and trnL-trnF intergenic spacers and rps16 intron) datasets of 7 taxa. For comparison of the relationships of A. canariense populations between the islands we used the ISSR method. We found that only one species of the section Molium occurs in the Canary Islands—the endemic species Allium canariense, closely related to Allium subvillosum. Independence of this new species has been confirmed by morphological and molecular features. Discussion on phylogeny, origin and geographic distribution is provided.