Wheat (Triticum aestivum) is being attacked by several fungal pathogens, many of them are seed-borne, infesting wheat seeds (grains) are detected by methods as recommended by the ISTA, 1966. Fungi such as Altenaria alternate, Aspergillus flavus, Aspergillus niger, Chaetomium spp, Cladosporium spp, Epicoccum spp, Fusarium spp, Fusarium oxysporum, Fusarium solani, Nigrospora oryzae, Penicillium spp, Rhizoctonia solani, Stemphyllium spp.and  Trichoderma spp. were isolated from the wheat cultivars i,e  Gemmiza 7, Gemmiza 10, Sids 1, Sids 12, Sakha 93, Sakha 94 and Bani sweif 1. Extracts of pomegranate, Neem and Garlic were screened for the potential antimicrobial activity through cup-plate method against three fungi (F. oxysporum, R. solani and A. alternata. All extracts showed inhibitory activites. F. oxysporum, R. solani and A. alternata were the greater portions of the isolated fungi. In vitro studies, seed treatment with 10, 20 and 30 % of concentration of plant extracts for 24 hours showed a complete germination and all seed testing. In vitro studies using cup-plate method were exercised to examine the antifungal activity of three plant extracts i.e., Neem, Pomegranate and Garlic against such fungi associated with wheat seed. F. oxysporum, R. solani and A. alternata were the greater portion of the isolated fungi. However, they were regarded of our main concern in order that they were known of their serious pathogens. Neem leaf extract showed good activity followed by pomegranate peeland garlic leaf extracts.  In vivo trials, results of the efficacy of plant extracts against the seed-borne pathogens were just about those cropped up in vitro practises.                 Effect of fungicides (Rizolex T 50 %) and three plant extracts on the incidence of seed-borne fungi and their effect on seed germination were evaluated. The seed treatment by the fungicides showed that (Rizolex T 50 %) increased the germination percentage and reduced seed mycoflora. Fungal properties of plant products were tested. Efficacy of biocontrol agent against (F. oxysporum, R. solani and A. alternata) was found good in controlling the seed-borne fungi and pomegranate was proved to be good inhibitor of fungi associated with wheat seeds. Thus, the seeds should be treated invariably by less phytotoxic fungicides like Rizolex T 50% and biocontrol agent like Pomegranate to eliminate the seed-borne mycoflora of wheat. The main aim of present study is to ascertain the fungal species and their effect on wheat grains germination.