Abstract: The causal pathogens of root rot and stalk rot of soybean were isolated from infected plants. Fusarium oxysporum, F. solani, Macrophomina phaseolina and Rhizoctonia solani were the main causal pathogens of pre- and post-emergence damping-off. The isolated fungi especially R. solani caused anatomically deformation in the basal portion of infected stem including complete disruption in epidermal cells and degradation of primary cell wall in cortical cells. The growth substances; Ethrel, Indole Butyric acid (IBA) and Cycocel (CCC) were tested in vitro on the growth of the pathogenic fungi. Ethrel at 200 ppm was the most effective in reducing fungal growth. During two successive growing seasons (2008 and 2009) of soybean under different salinity stress (1000 to 3000 ppm), the application of growth substances led to significant reduction in pre- and post-emergence damping-off as well as root and stalk rot diseases. Ethrel, CCC and IBA increased significantly branches number plant-1, photosynthetic pigments, total phenol, proline content, yield and seed quality (oil and protein %). Ethrel and CCC at 200 ppm were the best treatments. Soaking soybean seed in Ethrel, CCC or IBA at 200 ppm is recommended to be incorporated into the production program of soybean to decrease root and stalk rots and increase productivity and seed quality under salt stress conditions.