Background In this study, the potential of extracts and powders of green seaweeds, Ulva fasciata, and Enteromorpha flexuosa was evaluated as biocontrol against the pathogenic soil-borne fungi, Macrophomina phaseolina and Fusarium solani, infecting cucumber plants in Egypt. The antifungal activity of the algal extracts was evaluated in vitro against the pathogens mycelial fungal growth using five organic solvents. Results Obtained results indicated that mycelial growth inhibition was noticed with F. solani in all algal extracts tested. In M. phaseolina, all algal extracts did not inhibit the fungal growth but affected microsclerotia formation (the main source of the second infection). In the case of F. solani, the highest reduction (68.6%) was noticed, while the chloroform extract of U. fasciata inhibited the radial growth of F. solani to 2.5 cm when E. flexuosa inhibited the radial growth to 4.3 cm as compared with the control (8.0 cm). The gas chromatography-mass spectrometry and the infrared spectroscopy analyses revealed that iron-monocarbonyl, cyclononasiloxane, and their functional groups, including amine, ether, etc., might play a core role in the anti-fungal activity of the seaweed extracts used. Conclusion This work concluded that the macroalgae species with many unique antifungal properties components had an inhibitory effect against soil-borne cucumber diseases. The antimicrobial activity might be explored in the future in numerous diverse applications in agriculture and plant disease control, revealing their actions to control some plant fungal pathogens.