Variability among populations of Ziziphora clinopodioides Lam. subsp. bungeana (Juz.) was analyzed, to evaluate the level and distribution of differentiation among four distant populations from sub-humid, upper semi-arid and semi-arid bioclimates of Khorasan provinces, Iran. Analyses of variances and cluster analysis have been carried out to define the variability and significance of morphological differentiation. Morphological differentiation was correlated with ecological situations at the location of origination and a high variation among populations based on morphological traits was observed between the plants belonging to semi-arid populations vs. the sub-humid ones. Essential oil composition varied among populations. In all of the populations pulegone was the main component, followed by isomentone and thymol. The clustering, based on oil analysis generated two distinct clusters. Essential oils of the upper semi-arid and sub-humid populations were rich in Iso-menthone, while populations from the semi-arid bioclimate were characterized by high amounts of pulegone. The relatively low morphochemical diversity in the populations of Z. clinopodioides indicates that the maintenance of their evolutionary potential is at risk if population sizes are not maintained and if there is no protection of the habitats.