Salvia chloroleuca Rech. f. & Aell. is one of the perennial species of the Lamiaceae family in Iran, which has antimicrobial and antitumoural properties. In the current research, the morphological variables and hydrodistilled essential oils of two populations, from Polor and Neyshabur, of this species were evaluated. We studied 10 and 40 individuals for morphometrics and essential oils, respectively. Morphological data were analyzed using SPSS. Furthermore, the extracted oils were analysed using GC and GC/MS. The qualitative morphological characteristics were stable between the populations, while the quantitative ones highly varied. The one-sample variance test revealed significant differences for most of the studied features. The yielded oil highly differed between these populations. The first and second main groups of compounds were the same for both populations, but with different percentages. However, the third and fourth main groups of compounds were not similar. Furthermore, the main compounds of essential oil differed between the studied populations. The major compounds of the Polor population were: β-pinene (22.7%), α-pinene (18.3%), germacrene D (7.7%) and sabinene (6.6%). However, spathulenol (19.8%), bicyclogermacrene (11.4%), p-cymene (10.8%) and β-pinene (10.4%) constituted the major compounds of the Nyshabur population. In total, the Neyshabur population had higher amounts of sesquiterpene and oxygenated compounds than the other population. The results indicated that in this species the quantitative morphological characters and essential oils were strongly affected by environmental factors.