Isozymes were used to study the phylogenetic relationships of selected species, varieties, and cultivars of Allium. Highest and lowest number of isozyme banding patterns was observed in Malate dehydrogenase and Malic enzyme, respectively. No intraspecific diversity was revealed within A. sativum and A. porrum. A. cepa showed some intraspecific diversity. Dendrogram showed close relationship among A. sativum and A. porrum. A. cepa was grouped with A. stracheyi and A. tuberosum. Principal coordinate analysis showed some differences with the dendrogram. This study showed that isozyme was more helpful for studying phylogenetic relationships at the species level rather than at intraspecific level. © 2013 Taylor and Francis Group, LLC.