Management and transmission of four seed-borne pathogenic fungi namely, Colletotrichum trifolii, Rhizoctonia solani, Fusarium equiseti and F. incarnatum were investigated on alfalfa plants. The pathogenicity test on alfalf plant showed that R. solani and C. trifolii caused high percentages of rotted seeds and seedlings mortality (26.45, 26.1% and 31.6, 21.1% , respectively). However, no significant differences were observed between the treatments with F. equiseti and F. incarnatum when compared with the control treatment. Transmission of the pathogenic fungi from seed to mature plant of alfalfa was investigated in this study. Results indicate that the recovery percentages of the tested pathogens gradually decreased from root apex up to the first internodes below the shoot tip, but did not reach to the shoot apex. In order to control these fungi, different concentrations of sodium metabisulphite (SM), sodium salicylate (SS) and hydroquinone (HQ) were tested in vitro. Treatment with SM at 10 mM completely inhibited the growth of all isolated fungi. Under greenhouse conditions, soaking alfalfa seeds in a water solution of hydroquinone at 12mM showed to be the most effective treatment in reducing seed rot and seedling mortality percentages and increasing seedling survival percentages. Application of the tested treatments presented significant increases in growth parameters, photosynthetic pigments (chlorophyll a and b and carotenoids) in leaves and total phenol in alfalfa plants. This study therefore recomended the use of HQ and SM as potential and promising antifungal agents in the protection of alfalfa plants against the tested seed-borne fungi.