The five most common cultivars from the genus Allium cepa L. in Bosnia and Herzegovina (BiH) were analysed, focusing on Konjic onion. Seven SSR markers for genetic similarity analysis were used to address the genetic backgrounds. The polymorphic relationship between the SSR markers was analyzed by using Polymorphic Information Content (PIC) and Heterozygosity (H) by using the online available PICcalc program. For the complete data analysis and phylogenetic tree construction, the DARwin 6.0.13 software was used. The total number of obtained SSR alleles was 30 bands, where 56.7% were polymorphic with the range of allele size of 130 to 650 base pairs (bp). The mean polymorphic information content (PIC) was 0.435 and the expected heterozygosity (H) values ranged from 0 to 0.785. Jaccard's coefficient of similarity values ranged from 0.14 to 0.55. The results in this study represent the first genetic diversity data on the onion cultivars in BiH and show significant dissimilarity among the onion cultivars. This study confirmed that the molecular SSR analysis represents an efficient tool for Allium cepa L. landrace genetic similarity analysis.