Short-tooth sage (Salvia brachyodon Vandas) is an endemic and one of the rarest plant species of the Dinaric karst. Although older literature indicates its presence in more localities; only two have been confirmed at the present time; Mt. Orjen (border of Bosnia and Herzegovina and Montenegro) and Pelješac peninsula (Croatia). Due to its very narrow distribution and economically very interesting essential oil composition short-tooth sage might become more endangered in the future. The aim of this research was to determine and compare inter-and intra- population morphological diversity of the only two noted natural populations of short-tooth sage by analyzing 16 quantitative morphological traits. Pelješac population of short-tooth sage showed considerably higher values for traits related to habitus and plant height; while the Mt. Orjen population showed higher values for traits related to the calyx and higher occurrence of sessile glandular hairs on the flower pedicels. When interpreting the obtained results; we should consider the fact that the habitats on Pelješac peninsula and Mt. Orjen greatly differ. In order to get better insight into the diversity and differentiation of short-tooth sage populations and to define efficient protection measures an additional analysis of populations using molecular markers are recommended.