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Navicula arenaria Donkin 1861 is a marine microalga belongs to class of bacillariophycea. Recently, microalgae and their products are used as biological control of diseases caused by phytopathogenic fungi. This is considered environmentally ecofriendly method to overcome the plant damage caused by soil borne pathogenic fungi and thereby economic loss. Therefore, this study aimed to investigate in vitro the antifungal activity of N. arenaria isolate PS 31 extracellular and intracellular metabolites against two taxa of soil borne phytopathogenic fungi; Macrophomina phaseolina and Fusarium oxysporum. N. arenaria PS 31 hexane extract was the most effective extract on growth inhibition of both phytopathogenic fungi. There is no significant difference between miconazole and N. arenaria hexane extract of 5.6 mg/ml on growth inhibition of F. oxysporum. The inhibitory effect of hexane extract at 5.6, 4.2 and 2.8 mg/ml and ethyl acetate extract at 35% (v/v) was higher than controls. Ethyl acetate extract was effective on growth inhibition of M. phaseolina (29.67%). GC-MS analysis of N. arenaria hexane fraction revealed the presence of potent antifungal compounds such as Phenol, 2,2'-methylenebis[6-(1,1-dimethylethyl)-4-methyl-, di-n-octyl phthalate, cholestane-3,5-diol, 5-acetate,(3.beta.,5.alpha.), Cholestan-3-ol,(3.beta.,5.beta.)- and beta.-Sitosterol. These results suggest that N. arenaria hexane extract can be used in biological control of plant diseases caused by M. phaseolina and F. oxysporum.