Soil mycoflora play an important role in agricultural economy. Limited information is available on soil mycoflora under zero-tillage and conventional tillage technologies of the rice-wheat cropping system. In the rice-wheat cropping system, due to continuous cropping and reduced rotation, soil-borne pathogens have become increasingly significant in the yield decline. The current study was conducted to gain an insight into soil-borne fungi associated with rice and wheat crop in the rice-wheat cropping system under zero and conventional tillage technologies. Some 107 fungal species belonging to 54 genera were isolated from foliar, roots and soil of rice-wheat crops under zero-tillage and conventional tillage technologies by five types of media (general fungi, basidiomycetes fungi, food spoilage fungi, keratinophilic fungi and zoosproric fungi). Some 43 genera including 59 species were isolated for the first time from rice, wheat plants of zero-tillage and conventional tillage technologies. The fungi were categorized into four groups (pathogenic, saprophytic, toxin producing and beneficial). Aspergillus flavus was identified as the only toxin-producing fungus and isolated from both rice and wheat crops. Trichoderma spp. were isolated from both crops and Paecilomyces spp were isolated only from wheat fields and are known as beneficial fungi. Among the pathogenic fungi Bipolaris sorokiniana, Fusarium oxysporum and Rhizoctonia solani were isolated as pathogenic fungi both from rice and wheat soils. Alternaria trtiticina, Fusarium equiseti, F. grameniarum, F. poae, F. solani and Pythium sp. were isolated only from wheat fields whereas Nigrospora oryzae, Rhizopus oryzae and Sclerotium oryzae were isolated only from rice fields. Total fungal colony counts isolated from soil showed the almost same number of fungi in zero-tillage and conventional tillage technologies.