Greenhouse experiment was conducted to evaluate the pathogenicity of root rot fungi on faba bean plant. Lab. experiment was also conducted to study the effect of organic compounds and fungicide Rizolex-T50 on the linear growth of the tested pathogenic fungi. Two field experiments were also carried out to study the effect of organic compounds with different concentrations and fungicide Rizolex-T50 on reduction of root rot and enhancing some morphological, physiological characteristics and productivity of faba bean under saline affected soil conditions during 2013/2014 and 2014/2015 seasons. The results under greenhouse conditions indicated that all tested pathogenic fungi caused emergence damping-off. Rhizoctonia solani was the most effective in pre-emergence damping-off while, Fusarium solani gave the highest percentage of post-emergence damping-off. The pathogenic fungi caused anatomically deformation in root structure. Infected root with F. solani caused complete destruction of epidermal cells followed by degradation of cell wall in the cells of cortex.  In vitro, Rizolex-T50 completely inhibited the growth of the tested pathogenic fungi. On the other hand, chitosan at 8 g/L was the most effective in reducing fungal growth followed by proline at 200 ppm. In vivo, the application of organic compounds counteracted the harmful effects of salinity. Humic acid highly reduced pre- and post-emergence damping-off and subsequently increased field emergence %. The high level of proline (200 ppm) was more effective in increasing morphological measurements (plant height, No. of branches and leaves/plant) and photosynthetic pigments i.e. chlorophyll a, b and carotenoids. While, the high concentration of HA (2000 ppm) significantly increased No. of pods/plant, seed yield/plant and 100-seed weight. Chitosan gave the highest phenols content followed by proline treatment. The high increase in carbohydrate content occurred under low level of HA (1000 ppm), followed by high level of proline (200 ppm). The efficacy of the tested organic compounds in control of root rot disease was reflected on the plant causing increase in yield components. It is suggested that pre-sowing seed soaking with HA (2000 ppm) or chitosan (8 g/L) or proline (200 ppm) could be considered as alternative fungicide for controlling root rot disease and increasing productivity of faba bean under salinity and natural infection conditions in the field.