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Salvia is an important genus of Lamiaceae which phenolic compounds are the main secondary metabolites of its members. The objective of this study was to investigate the diversity of phenolic and flavonoid compounds in the leaves and flowers from 41 wild populations of 27 Salvia species from Iran by TLC method and evaluation of their significance as chemical markers for taxonomic purposes. Rosmarinic acid, salvianolic acids A and B, apigenin, rutine, scutellarin and baicalin were characterized as the main compounds of the studied Salvia species. Based on the dendrogram obtained from the didtribution patterns of phenolic compounds using cluster analysis by UPGMA method, the Salvia species were studied chemotaxonomically. Results showed that the patterns of phenolic compounds in the leaf and flower organs were similar in populations of a species, while they were different among the species. It seems that substantial differences in the patterns of these compounds at inter-species level were mainly due to genetic differences. The results from classification of the species by cluster analysis of the phenolic data supported their grouping according to their classical taxonomy in the Flora Iranica. This suggests the importance of these compounds as chemical markers for the classification of Salvia species at inter-species and subgenus levels.