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ABSTRACTIn this study, inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) markers were used for genetic diversity and relationship analysis of nine Salviaspecies. Twenty-one and twenty selected ISSR and SCoT primers amplified 350 and 329 loci, respectively, of which all were polymorphic. The obtained average polymorphism information content (ISSR, 0.38; SCoT, 0.40), average band informativeness (ISSR, 16.67; SCoT, 16.45) and resolving power (ISSR, 9.75; SCoT, 12.52) revealed high genetic diversity prevailing among Salviaaccessions. Considering the ISSR and SCoT data, the species with a basic chromosome number of x= 8 showed higher values of the percentage polymorphism loci (PPL), the number of observed alleles (Na) and Shannon index (I) than the other species. The partition of clusters in the neighbour-joining dendrogram based on ISSR, SCoT and combined data was similar and grouped all individuals into four clusters. However, the dendrogram generated based on SCoT separated the individuals into sub-clusters in accordance with their species and section. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and SCoT techniques, the correlation coefficient (r) was 0.83, and the results showed that both techniques were effective to assess the genetic diversity. Our results indicated that SCoT markers can be used as a reliable and informative technique for evaluation of genetic diversity and relationships among Salviaspecies.