In this study, the effects of aqueous extracts from Zygophyllum fabago L. on two plant phytopathogenic fungal species (namely, Fusarium oxyosporum f. sp. melonis and Pythium aphanidermatum) were studied under laboratory conditions. The plant extracts (10% w/v) were prepared by using deionized water and fresh tissues. Dilutions (2, 4, 6, and 8% w/v) were obtained to test their effect on the mycelial growth of the phytopathogenic species. Additionally, the recovery of the fungi after their exposure to the Z. fabago extract was analyzed. The plant extracts inhibited the growth of F. oxyosporum and P. aphanidermatum (the maximum mean inhibition that was recorded with the 10% w/v extracts was 42.9% and 85.3%, respectively). A second series of experiments demonstrated the existence of residual effects in both species. The amount of residual inhibition by the 10% w/v extracts was 28.6% in F. oxyosporum and 53.8% in P. aphanidermatum. A dose-response was clearly observed in P. aphanidermatum, while an increase in extract concentration was not associated with a significantly greater reduction in the growth of F. oxyosporum. These findings give insights into the potential of Z. fabago as a growth inhibitor of F. oxyosporum and P. aphanidermatum, thus suggesting an interesting potential role for this common weed as a source of natural fungicides.