In Oman, the farming system in the majority of farms follows a conventional system, which is characterized by growing multiple crops mainly for home consumption, but also for local market and sometimes for export. In addition, some farms have started recently adopting organic farming. This study was conducted to assess fungal diversity in the rhizosphere of crops under conventional and organic farming systems in Oman and also to investigate for the potential presence of antagonistic fungal species that can be used in future biocontrol programs. The first part of the study dealt with evaluating the efficiency of direct plating in comparison to pyrosequencing in estimating fungal diversity in soil, Analysis of 10 soil samples collected from two farms in Oman showed that pyrosequencing detected More ara significantly more fungal phyla, classes and genera compared to direct plating. Pyrosequencing detected five unique fungal classes that were not recovered by direct plating. This could be related to the ability of pyrosequencing to detect uncultivable and slow growing fungal species. The second part of the study analyzed fungal diversity in conventional and organic farms growing cucumbers and tomatoes using pyrosequencing. Pyrosequencing results revealed that fungal diversity varied between the different cultivation systems. Richness estimates indicated that soils from the organic farms have higher fungal diversity compared to soil from conventional farms. Ascomycota and Microsporidia were the most dominant fungal phyla in most of the samples. Other dominant phyla included Chytridiomycota and Basidiomycota, Microsporidetes, Dothideomycetes, Eurotiomycetes and Leotiomycetes were the common classes in most soil samples. Five and four unique classes were detected in the rhizospheres of cucumber and tomato grown organically, respectively. The differential level of fungal diversity within and among farms could be related to the variation in the cultural practices employed. It also shows that organic farming favors higher levels of fungal diversity. The last part of the study examined the biocontrol potential of 36 fungal isolates obtained from the rhizospheres of tomato and cucumber in Oman against Pythium aphanidermatum and Rhizoctonia solani, the causal agents of damping-off of cucumber. In vitro screening of the 36 fungal isolates against P. aphanidermatum and R. solani showed that isolates TO144 and TT266 were the most effective in inhibiting the mycelial growth of P. aphanidermatum and R. solani. Inoculation of cucumber seedlings with the antagonistic isolates TO144 and TT266 did not have any negative effects on the survival of cucumber seedlings. Isolate TT266 significantly improved dry weight of cucumber seedlings compared to the control (P < 0.05). The two antagonistic fungal isolates significantly increased the survival of cucumber seedlings inoculated with P. aphanidermatum from 7% to 62% when T0144 was used and to 38% when TT266 was used. In addition, they also significantly increased the survival of cucumber seedlings inoculated with R. solani from 15% to 31% when T0144 was used and to 69% when TT266 was used. Identification of TO144 and TT266 to the species level using sequences of the ITS region showed that they are Trichoderma asperellum and Talaromyces pinophilus, respectively. This is the first report of the potential of Talaromyces pinophilus as a biocontrol agent for Pythium and Rhizoctonia damping-off of cucumber. The study also shows that fungal isolates present in the rhizosphere of vegetable crops can be potential biocontrol agents for soil borne diseases.