This study sought to measure genetic diversity and phylogenetic structure among 196 individuals of saffron from 20 geographically separate accessions from Iran, Spain and Turkey using retrotransposon derived iPBS markers. Twenty-eight primers amplified a total of 179 polymorphic alleles with an average of 6.4 bands per primer. The average of parameters shannon's information index, genetic distance and gene diversity was 0.483, 0.286 and 0.841 respectively. Polymorphic information index ranged from 0.407 to 0.953 with an average of 0.824. Primers 2298, 2229 and 2393 with 0.953, 0.943 and 0.943 PIC respectively, identified as the most informative primers in this study. The results of phylogenetic trees showed that twenty saffron accessions were placed into four major clusters that matched with their geographical locations completely. These results are supported by principal coordinate analysis. Overall, we can confirm that iPBS markers as low cost and high efficient molecular markers are a powerful DNA fingerprinting for assessing genetic diversity and phylogenetic analysis among saffron accessions originating from different geographical regions.