In this study, molecular markers were used for the first time to study the genetic diversity of Turkish onion (Allium cepa L.) accessions. We used 83 turkish landraces, 3 breeding lines and 10 commercial varieties, in total 96 accessions, to study the genetic diversity. Bulked samples of 10 seeds were used to generate a representative profile of the accessions. Variability was evaluated at 46 microsatellite loci. We identified 308 alleles with these markers, out of which 303 were polymorphic. A dendrogram based on the UPGMA analysis grouped the 96 accessions into five main clusters. Dice's similarity coefficient ranged from 0.407 to 0.767 with an average of 0.587. The results showed that 44 out of the 46 SSR markers were convenient and polymorphic enough to distinguish all the studied accessions.