In this study, we evaluated the chemotaxonomic status and chemical diversity of Salvia L. species in Iran using leaf flavonoid profiles. From natural habitats in the country, we collected samples of 14 species of the genus: S. spinosa L.; S. macrosiphon Boiss.; S. reuterana Boiss.; S. sharifii Rech.f. & Esfand.; S. nemorosa L.; S. virgata Jacq.; S. syriaca L.; S. mirzayanii Rech.f. & Esfand.; S. atropatana Bunge; S. limbata C. A. Mey; S. sclarea L.; S. ceratophylla L.; S. multicaulis Vahl.; and S. hydrangea Dc. ex Benth. Two-dimensional maps of these species were created with thin-layer chromatography. In order to study the taxonomic position of these species and 37 accessions, cluster analysis was applied. The results of the cluster analysis showed that S. spinosa was distinct from S. reuterana. Despite considerable morphological similarity between S. nemorosa and S. virgata, those two species are definitely distinguished. In addition, S. spinosa and S. macrosiphon were roughly grouped, whereas S. ceratophylla and S. multicaulis composed two separate groups. In the 14 species collected, the flavonoids identified were flavones, flavonols, flavanones, isoflavones, dihydroflavonols and chalcones. We found that flavonoids are appropriate indicators to determine the taxonomic position of Salvia species.