Endophytic fungi have recently been proven to possess active secondary metabolites, especially those colonizing medicinal plants like Salvadora persica. Eight endophytic fungi were isolated from S. persica, (Gliocladium catenulatum, Paecilomyces variotii , Penicillium bravicompatum , P. jensenii, Aspergillus fumigatus, A. parasiticus , A. niger and Verticillium albo-atrum). Six of these endophytes showed antagonistic activities against important plant pathogenic fungi, Fusarium verticilloides (5.91-18.23%), Alternaria alternata (10.5- 31.09 %) and Cochliobolus spicifer (16.94-28.93%) inhibition percentage in dual culture assay. The antimicrobial activity crude extracts of ethyle acetate and n-butanol of both G. catenulatum and P. variotii with three different concentrations (0.5 mg/ml,1.0 mg/ml, 2.0 mg/ml) were tested against the pathogenic fungi. Generally, ethyl acetate extract of both endophytic fungi had an inhibition effect on the pathogen growth higher than n-butanol extract. Thus, this is the first report to evaluate the antifungal effect of S. persica associated fungi as a biological control against fungal plant pathogen.