In the present study, we used 39 plant samples representing six Carthamus taxa collected from different regions of Turkey: 11 of C. dentatus, 5 of C. glaucus, 18 of C. lanatus, 3 of C. persicus, 1 of C. tenuis subsp. tenuis and 1 of C. tenuis subsp. gracillimus. On these samples, we screened nine ISSR markers for polymorphic products. We generated 151 polymorphic bands. In a dendrogram based on these ISSR bands, the first branch was C. tenuis subsp. gracillimus, then C. persicus formed the second group. The rest of the taxa were grouped in two clusters: the first included C. lanatus, C. tenuis subsp. tenuis and C. glaucus, and the second included C. dentatus. Within the first cluster, C. tenuis subsp. tenuis and C. glaucus grouped together and then united to C. lanatus. Representatives of the same taxa consistently clustered together. Also within species, the groupings were generally concordant with their geographical distributions.