Various fungi were isolated from sunflower seed samples collected from two fields in Ismailia and Beni-Suef governorates. Fifteen fungal species belonging to 10 genera were isolated from Beni-Suef fields and thirteen fungal species belonging to 8 genera were isolated from Ismailia field. Alternaria alternata recorded the highest frequency from sunflower seed samples collected from the two locations followed by Aspergillius flavus and A. niger. Macrophomina phaseolina was the main seed-borne pathogen isolated from sunflower seeds collected from the two locations followed by Fusarium oxysporum and Fusarium spp. Applying thermo-treatments through microwave radiation in five exposing periods (15, 30 sec, 1, 2 and 4 min.) and hot water treatment at five soaking periods (30 sec, 1, 2, 4 and 8 min.) gave significant impacts on the occurrence of seed-borne pathogen M. phaseolina in sunflower seeds as well as seed germination. Moreover, increasing the exposure time of microwave radiation or soaking in hot water led to enhancing their effects. Soaking in hot water negatively affected thefrequency of M. phaseolina than microwave radiation treatment. Generally, the obtained results clearly show that microwave radiations and hot water treatments significantly decreased the incidence of pre- and post-emergence damping-off. Moreover, sunflower seeds exposed to either treatment then planted under greenhouse conditions in infested and non-infested soil with M. phaseolina or under open field conditions, naturally infested, led to increase of sunflower seed yield. In this respect, the highest impact was obtained when sunflower seeds were soaked in hot water at 2 min followed by soaking in hotwater for 1 min and exposure to microwave radiation for 1 min. Data also proved that the efficiency of some thermal treatments was approximately close to efficiency of fungicide in reducing damping-off and charcoal rot diseases during 2017 and 2018 trail seasons, where soaking in hot water for 2 min. was the closest one.