Abstract: Salvia L. belongs to Lamiaceae family, have 900 species around the world. Seven of them distributed in Mashhad (North-East of Iran) which are following: S. spinosa L., S. staminae Montbr and Auch, S. sclarea L., S. chloroleuca Rech and Aell., S. virgata Jacq, S. chorassanica Bung. and S. nemorosa L. In present research seed proteins of Salvia sclarea L., S. spinosa L. and S. chloroleuca Rech and Aell. studied by sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE) method. The aim of present study was identifying the variation between seed protein in populations and relationship with morphological characters and geographical distance. Analysis showed 22 bands from which some of them were specific for a population. Cluster analysis of populations were carried out. The variation bands have correspondence to geographical distance and morphological characters.