RAPD and ISSR markers have been used to reveal the genetic diversity and phylogenetic analysis of some economically important species of Allium. Two plants related to Allium were also included for better understanding of the phylogeny. ISSR showed more polymorphism within A. cepa and A. sativum, while RAPD showed more polymorphism within A. porrum. Overall, RAPD revealed more intraspecific diversity than ISSR, while ISSR showed more interspecific diversity than RAPD. This showed the usefulness of using both markers for the study of Allium. UPGMA-based dendrograms showed a close relationship between Allium sativum and Allium porrum. A. porrum showed less genetic variability than A. cepa and A. sativum. Several unique bands were identified with RAPD and ISSR, which can be converted into cultivar-specific markers. Principal coordinated analysis, however, showed some minor differences with UPGMA-based dendrograms. This study showed that rapid and cost-effective markers like RAPD and ISSR coupled with appropriate statistical tools can be successfully applied to study phylogenetic relationships at the interspecific and intraspecific level in Allium. These markers proved to be suitable for both phylogenetic studies among different species as well as for characterisation of different cultivars of Allium. © TÜBİTAK.