The biocontrol potential of eight isolates of endophytic fungi species and ten isolates of endophytic yeast with seaweed (Melanothamnus afaqhussaini) a red algae belongs to Rhodophyta have shown significant reduction on infection of root rotting fungi (Fusarium oxysporum, Rhizoctonia solani, Macrophomina phaseolina, and Fusarium solani) were evaluated in pots for their effect on root diseases of sunflower, their growth, and induction of systemic resistance. Aqueous suspensions of endophytic fungi and yeast with combine application of seaweed (Melanothamnus afaqhussaini) were applied in pots using sunflower as test plant. Carbendazim a fungicide served as positive control. Data on the fungal infection of roots, plant growth, plant resistance markers like polyphenol, salicylic acid and antioxidant status of plant were determined. These isolates significantly suppressed root diseases and induced systemic resistance via increasing level of resistance markers, polyphenol and salicylic acid besides improving antioxidant activity of endophytic fungi and yeast with combine application of seaweed (Melanothamnus afaqhussaini)-treated plants as compared to control plants. Endophytic fungi and yeast with seaweed (Melanothamnus afaqhussaini) have potential against common root-infecting fungi of sunflower and can improve plant growth. Endophytic fungi species and endophytic yeast can suppress root rotting fungi by direct mechanism or induction of systemic resistance in plants.