Ion balance and osmotic regulation in plants to mitigate the effects of drought is possible with accumulation of osmolytes like proline and glycine betaine. Accordingly, in order to investigate the effect of mycorrhizal fungai species on the eco-physiological characteristics of hyssop, a factorial experimental based on randomized complete block design with three replications was conducted at the Research Farm of Agriculture and Natural Resources of West Azarbaijan in 2013. Experimental treatments included species of mycorrhizal fungi (Glomus mosseae, G. intraradices, G. fasiculatum, G. claroideum, Acaulospora longula and control without mycorrhiza) and four levels of irrigation (irrigation at 80, 70, 60 and 50% of field capacity). The results of ANOVA showed the significant interaction between water deficit and mycorrhizal fungi species on the concentrations of malondialdehyde (MDA), glycine betaine, proline, total soluble carbohydrates and essential oil percent. The highest concentrations of malondialdehyde (MDA) (125 nmol/g fresh weight), glycine betaine (2019 mm/g dry weight), proline (111 mm/g fresh weight), essential oil percentage (7.29%) and total soluble carbohydrates (396.7 mg/g dry weight) were obtained from plants inoculated by G. claroideum, A. longula, A. longula, G. fasiculatum and G. claroideum and irrigated at 50 and 60% field capacity, respectively. The concentration of malondialdehyde (MDA) biomarker was increased at non-mycorrhizal plants compared with mycorrhizal one. Overall, this study suggested that the mycorrhizal species were effective to reduce stress and water use efficiency.