In order to study the effects of drought stress and mycorrhiza fungi on establishment rate and some growth-morphological traits of Ziziphora clinopodoides, pot experiments were conducted as factorial design based on a completely randomized design at the research greenhouse of agricultural faculty, Ferdowsi University of Mashhad in 2014; pots were combined as four levels of drought stress including 100 (Control), 75, 50 and 25% of Field Capacity (FC) and three levels of mycorrhiza fungi including Glomus intraradices, Glomus versiforme and control. The results showed that drought stress of 25%FC decreased plants weight (0.75, 0.67 and 0.19g/pot), plant height (1.25, 1.18 and 0.7cm), establishment rate (67.50%, 57% and 14.25%) and plants root colonization by mycorrhiza fungi (50%, 35.5% and 0) by the application ofG. intraradices, G. versiforme and control, respectively indicating significant effects of bothMycorrhiza species on drought resistance. Result indicated that the establishment rate was decreased significantly to 85%, 64% and 36% usingG. intraradices, and G. versiforme and control at 50%FC, respectively. Similarly, the establishment rate was reduced in the inoculated plants with mycorrhiza treatments less than control (67.50%, 57% and 14.25% at 25%FC) so that symbiosis of Mycorrhiza fungi significantly improvedZ. clinopodoides establishment rate under drought stress against the control. The effect of G. intraradices and G. versiforme on plants establishment rate (93% against 78.50% at 75%FC), plants height (5.93cm against 5.30cm at 75%FC) and dry weights (1.07g against 0.95g at 50%FC) was higher through drought stress. The Glomus intraradices reacted better to mild drought than G. versiforme and increased the establishment and morphological traits of plant. According to results, G.intraradicescould be introduced as a biological fertilizer and a technique for retrofitting and increasing tolerance of Z. clinopodoides against drought stress.