To investigate the effects of drought stress on morphology of Salvia sclarea, this experiment was conducted in 2011 in Alborz Research Station, dependent of Research Institute of Forests and Rangelands, Karaj, Iran. The experiment was conducted in split plot in the form of a randomized complete block design with three replications. The main plots were irrigation (at 30 and 60% of field capacity along with a well watered control). The sub plots were three Salvia sclarea populations (Esfehan; Semnan and Karaj). The results showed that drought stress had significant effect on dry matter yield, lateral root numbers, root length, the longest lateral root, root diameter, root volume, plant height and also leaf length and width. Moreover, population had significant effect on dry matter yield and plant height. Among all the measured samples, Karaj population had the highest dry matter yield and plant height; however, Isfahan population had the lowest value of the mentioned traits. Meanwhile, the control produced the highest dry matter yield (724.78 kg/ha), root diameter (10.48 cm), plant height (47.88 cm), leaf length (38.03 cm) and leaf width (19.5 cm). The lowest values of the mentioned traits were achieved in 30% of FC. The longest root (49.21 cm) was observed in 60% of FC and the shortest one (34.11 cm) was recorded in 30% of FC. Karaj population × control produced the highest dry matter yield, number of lateral roots, root diameter, root volume, plant height and leaf length and width. Therefore, Karaj population could be introduced as suitable Salvia sclarea population in Karaj region.