The response of Thymus vulgaris and Zataria multiflora to mycorrhiza fungus inoculation (inoculation and non-inoculation with Funneliformis mosseae) at different irrigation levels (irrigation 100% of field capacity (100% FC, control or no stress); 75% FC (moderate stress); and 50% FC (severe stress); was investigated in greenhouse conditions. The results showed that inoculation with mycorrhiza led to improvement of root volume by 100%, root dry weight by 159%, shoot fresh and dry weight by 77% and 96%, and water use efficiency by 98% under 100% FC and in some cases under 75% FC. The results of evaluating the mycorrhizal inoculation effect in different irrigation conditions, also showed that the effectiveness of mycorrhizal inoculation decreased dramatically with increase in stress intensity. Phosphorus (P) content of the shoot of T. vulgaris and Z. multiflora decreased with drought stress application. In addition, mycorrhizae inoculation increased root P content by 14% in T. vulgaris. In Z. multiflora, inoculation with mycorrhizal improved P content by 63% compared with non-inoculation under severe stress. While in T. vulgaris, root P uptake was improved (170%) by mycorrhizal inoculation under normal and mild stress conditions, mycorrhizal inoculation did not show the efficiency to improve P uptake under severe stress condition. Meanwhile, in Z. multiflora, P uptake was improved by 75% and 215%, respectively in mycorrhizal inoculation under 75% and 50% FC. This can be one of the most important reasons for reducing the shoot to root ratio by mycorrhizal inoculation under severe stress conditions.