Salvia (sage) is a species rich and medicinally important genus. Species-level identification is usually very difficult, particularly in closely related species. Here, we investigated nutlet micromorphological characteristics of 51 taxa belonging to S. subg. Salvia, S. subg. Sclarea and Salvia verticillata clade (S. subg. Heterosphace) by stereo binocular microscopy and scanning electron microscopy to show their taxonomic and phylogenetic value. The present study is the most comprehensive nutlet micromorphological study based on the number of taxa studied in the genus so far. The size of nutlets varies from 1.61 mm (S. verticillata subsp. verticillata) to 8.44 mm (S. albimaculata) in length, 1.02 mm (S. verticillata subsp. verticillata) to 4.20 mm (S. macrochlamys) in width. Nutlet length/width ratio ranges from 1.02 (S. bracteata and S. indica) to 3.06 (S. albimaculata). The basic shape of nutlets is elliptic, widely elliptic, circular, ovate or obovate. Five nutlet sculpturing patterns are present namely colliculate, reticulate, verrucate, rugose and foveate. The variation of surface sculpturing, nutlet shape, size, and exocarp cell shape provide useful diagnostic properties at species and subgenus level. However, nutlet micromorphological characters are of low phylogenetic value in studied Salvia species.