The use of antagonist microorganisms against pathogenic organisms in organic agricultural systems was promising for biological control approach. The aim of this study was to determination of the potential biological control of some fungal isolates which characterized as endophytic and antagonistic against soil borne Fusarium culmorum (FC) and F. oxysporum f.sp. radicis lycopersici (FORL) pathogens. For this, seven isolates of endophytic Acremonium spp. that isolated from healthy wheat plants and eight isolates of antagonist Trichoderma spp., isolated from soil of organic vegetable areas, were performed as biological control agents (BCA). The agar media with hypha and mycelia of the BCAs and spore suspensions (106 spores/ml) of FC and FORL were treated for inoculation of wheat seeds and tomato seedlings. The harvested plants were statistically analyzed by some parameters (severity of crown rot disease (%DS and scale), plant lengths (cm) etc.). In conclusion, the Acremonium isolates (47.5%) were lower means of disease severity than Trichoderma isolates (74.6%) for FC and FORL assessments in wheat experiment. In tomato, the averages of disease severity between Acremonium and Trichoderma were similar while their means were lower than positive control (The Scale of DS=0.67