Since the middle ages, essential oils have been widely used for fungicidal, bactericidal, virucidal, anti-parasitical, insecticidal, medicinal and cosmetic applications, especially nowadays in pharmaceutical, sanitary, cosmetic, agriculture and food industries. This study was undertaken to explore the effect of essential oils from Satureja hortensis, Origanum vulgar, Cinnamomum zeylanicum, Allium hirtifolium and Anethum gravcolens against two well-known plant pathogenic fungi, Fusarium moniliforme and F. graminearum. In addition some observations were made using microscopic scanning (MS) to detect possible alterations on the hyphal growth. The data of mycelium growth recorded at 5 days after inoculation at 27±1°C show that Satureja hortensis essential oil perfectly inhibited growth of both fungi tested at concentration 100ppm in PDA medium. Origanum vulgar, Cinnamomum zeylanicum, Allium hirtifolium oils were effective at concentration 800ppm and Anethum gravcolens oils had no effect. MS observations revealed alterations in the growth pattern of hyphae when the essential oil of Satureja hortensis was present. These results indicate that essential oil of S. hortensis could be used for management of these pathogens as a potential source of sustainable eco-friendly botanical fungicides.