Abstarct: Inoculum of materials baxsed on the use of micro-organisms stimulating plant growth will be keys to the future of sustainable agriculture. Use of high levels of chemical fertilizers resulted severe environmental contamination, such as soil and water pollution. Organic fertilizers are used to decrease the pollution. In order to study the effect of mesorhizobium bacteria and mycorrhizal fungi on the yield and yield components of cowpea under water deficit condition, an experiment was carried out during 2012 in field conditions as a spilit plot factorial on the basis of completely randomized block design with 16 treatments and 3 replications at Agriculture Research farm of Shahrood University. The main plot was water deficit condition (D) at four levels: d1 (no-irrigation), d2 (no-irrigation at 50 percent of flowering stage), d3 (no-irrigation at 50 percent of pod formation) and d4 (no-irrigatio at 50 percent of filling grains period) respectively. Mycorrhizal fungi(Glomus intraradices) at two levels (inoculated and non-inoculated) and two levels of rhizobium bacteria (Mesorhizobium) inoculated and non-inoculated) were considered as subplots factors. The results showed that water deficit stress reduced plant height, stem diameter, number of lateral branches, ground first pod distance, pod length, leaf dry weight, shoot dry weight, dry weight of pods, Number of pods per plant, seeds per pod, seed weight, leaf area index, plasma membrane stability, yield and harvest index However were no significant effect on the other characteristics such as (number of nodule, nodule weight, nodule dry weight, percent of root colonization, chlorophyll and phosphorus of soil). The combination of stress and fungi were significant on first pod distance, leaf dry weight, shoot dry weight, dry weight per pod, seed weight, seed yield, biological yield, harvest index, and the stability of the plasma membrane but they were no significant on the other characters. Interaction between stress and bacteria had no significant difference on the morphological characteristics such as: the first pod distance, number of pods per plant, pod dry weight, grain yield, and harvest index, number of nodules, nodule fresh weight and leaf area index than the control sample. Application of mycorrhizal fungi also significantly increased the percentage of root colonization in cowpea. In this study co-incolution of fungi and bacteria reduced damage caused by deficit irrigation and they could increas yield.