To achieve sustainable development, effective microorganisms (EMs) are widely used as a tool for agriculture and forestry sector in recently. EM is a commercial bio-fertilizer that contains a mixture of co-existing beneficial microorganism such as photosynthetic and lactic acid bacteria, yeast and actinomyces. The present study was conducted to evaluate the effect of EM application on seedling morphological and physiological characters of Taurus cedar seedlings. In the research, four different EM (EM-1, EM-A, EM-5 and EM-GOLD) with different dozes (Control-low-medium-high; Control-10%, 30% - 20%, 60% - 30%, 90%) applied on seedlings and potting. Morphological and physiological characters were determined as to measurements and calculations made in 3+0 aged containerized seedlings of Taurus cedar (Cedrus libani A. Rich). Morphological characters such as seedling height (SH), root collar diameter (RCD), number of branches (NB), number of buds at terminal shoot (NBTS), root length (RL), stem fresh weight (SFW), root fresh weight (RFW), total seedling fresh weight (TSFW), stem dry weight (SDW), root dry weight (RDW), total seedling dry weight (TSDW), dry root percentage (DRP), Sturdiness quotient (SI), SDW/RDW ratio, Dickson quality index (DQI) and physiological characters such as chlorophyll a, chlorophyll b, total chlorophyll (a + b), relative humidity (%) and transpiration rate are examined. For analysing of the data, multiple tests were used with variance analysis. As a result of the research; EM applications significantly enhanced of RCD and SI positively. In addition, EM1 application effected on DRP more positively according to Control and the other EMs applications. EM applications effected on chlorophyll a, chlorophyll b, total chlorophyll (a + b), relative humidity (%) and transpiration rate, significantly. However, EM applications were not found statistically significant on SH, SFW, TSFW, SDW, RDW, TSDW, and RL. In general, it has been concluded that EM applications are more effective than the morphological characters on the physiological characteristics of seedlings.