Abstarct: Water deficit is one of the inhibitors of agricultural production. Since the global approach in the production of medicinal plants is effective in improving the quantity and quality of effective substances, it seems that the healthy nutrition of plants through the use of biofertilizers is most in line with the goals of medicinal plant production. In order to investigate the effect of of bio- fertilizers and non- bio fertilizers on yield and some physiomorphological Thymus vulgaris traits on water deficit stress, During 2017-18, Experiment was conducted as a split plot baxsed a randomized complete block design with three replications in the Askariyeh field in Yazd. Experimental treatments including water deficit stress at three levels including W1=7(Control), W2=12 and W3=17 days irrigation interval as a main plot and bio and non bio fertilizers at five levels including B1=control(without fertilizer),B2=Endomycorrhizal (Glomus mosseae,G.intraradics, G.etunicatum),B3=Azospirillum brasilense,B4=Pseudomonas fluorescens and B5= chemical fertilizer(NPK) were the sub plots.The results of combined analysis showed that, the interaction of the year, water deficit stress fertilizers was significant in terms of on flavonoid and protein contents. The second year, had more lavonoid and protein levels than the first year.At stress levels from W1 to W3, the amount of flavonoids was increased while the amount of leaf protein was reduced. Meanwhile, Pseudomonas was more efficient at the W3 stress level. The interaction of water deficit stress and biological and non-biological fertilizers had a significant effect on flowering branches yield and biological yield. So that, with increasing the level of water deficit stress, their amount was reduced by 63%. Mycorrhiza and Azospirillum fertilizers were more effective in these conditions, respectively. Also, the interaction of water deficit stress and biological and non-biological fertilizers had a significant effect on total leaf chlorophyll content. with increasing the level of water deficit stress,¬the total chlorophyll content of the leaves decreased by 54%. At the highest level of water deficit stress, the use of Pseudomonas ameliorated the adverse effect of water deficit stress on the reduction of total chlorophyll in the leaves of thyme.About the percentage of essential oil and essential oil yield, simple effect of water deficit stress and biological and non-biological fertilizers on the percentage of essential oil and interaction of water deficit stress and biological and non-biological fertilizers on essential oil yield were significant. So that water deficit stress at the highest level increased it by 31%. Among biological and non-biological fertilizers, mycorrhiza and pseudomonas fertilizer had a greater effect on the percentage of essential oil and essential oil yield respevtively . In the case of the two elements nitrogen and phosphorus, the results of combined data analysis showed that the interaction of water deficit stress and bio- and non-bio-fertilizers had a significant effect on the concentration of these two elements in thyme leaves and caused a decrease in their concentration in the leaves by 54% and 59%, respectively. Azospirillum had a greater effect on water deficit stress in relation to the concentration of these two elements in thyme leaves. water deficit stress increased the amount of proline and soluble sugars in the leaves as well as the activity of antioxidant enzymes such as catalase, peroxidase and superoxide¬dismutase in the leaves of thyme and among biological and non-biological fertilizers, Pseudomonas fertilizer had a greater effect on these compounds. In general, from the results of two years of experimentation, it can be concluded that although water deficit stress reduces biological yield, yield of flowering branches and the amount of photosynthetic pigments (chlorophyll "a" and chlorophyll "b"),But in general, the use of Pseudomonas fertilizer by improving physiological and biochemical traits, improved the growth , biological yield and flowering branches yied.The use of biofertilizers, especially Pseudomonas fertilizer can greatly reduce adverse effects of water deficit stress.Therefore,the use of Pseudomonas in of water deficit stress conditions in this plant is recommended.