Water deficiency is one of the most important factors for limiting crop yield in arid and semiarid regions. Symbiosis with a variety of microorganisms in these regions is one of the modern ecological approaches for sustainable agriculture to reduce damages caused by environmental stresses. Symbiotic of arbuscular mycorrhizal fungi (AM) with the roots of crops has shown positive effects on agricultural systems. In order to study the effects of inoculation with two species of mycorrhizal fungi and irrigation levels on root growth criteria and water use efficiency of corn, an experiment was performed as split plots based on a complete randomized block design with three replications at the Agricultural Research Station, Ferdowsi University of Mashhad during growing season of 2008-2009. Treatments included two mycorhizae inoculation (Glomus mosseae and G. intraradices and control) and four irrigation levels (25, 50, 75 and 100% of water requirement). Grain yield, root specific length, the percentage of root colonization and water use efficiency based on grain yield of corn were measured. The results showed that the effect of mycorrhizae inoculation was significant on (p≤0.05) root specific length, grain yield and water use efficiency of corn. Mycorrhizae species had no significant effect on root colonization percentage of corn. Different irrigation levels had significant effect on grain yield, special length root, the percentage of root colonization, and water use efficiency of corn (p≤0.05). Generally, the results showed that mycorrhizae inoculation in water deficiency conditions, can increase the uptake of water and nutrients by developing the root and increasing the absorbing surface. In this way, not only the plant tolerance against the water deficiency increases, but also more yield will be produced for a specific value of water, which means the water use efficiency increases. Furthermore, the use of water will be decreased.