Effective microorganisms (EM) is a commercial biofertilizer mainly consists of photosynthetic and lactic acid bacteria, yeast and actinomycetes. In order to evaluate the influence of EM (0 and %1) and salt stress (0 mM, 50 mM, 100 mM and 150 mM) on the morphophysiological characteristics of pomegranate cv. shishe-kap, a factorial experiment was conducted based on the completely randomized design at the research greenhouse of Ferdowsi University of Mashhad. NaCl (10 part) and CaCl2 (1 part) were utilized to exert the salinity stress. Studied parameters included the main stem height, shoot fresh weight, root length, root dry weight, root volume, leaf relative water content, electrolyte leakage, chlorophyll index, potassium and sodium contents. The results showed that all the measured morphophysiological parameters expect the electrolyte leakage were significantly higher in EM treatment in comparison to no EM treatmant in saline conditions. In addition, under the extreme salinity stress (150 mM), application of 1% EM decreased the sodium content of to 12.5% and increased the potassium content to 11.5%. According to the obtained results from the above parameters, it seems that EM can reduce the harmful effects of salinity.