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Wheat is the most important cereal produced in Iran. A mycological survey was carried out for the first time, on the stored wheat samples in Tehran, East Azarbayejan and Mazandaran provinces in 2007. Exogenous and endogenous fungi, were isolated by the method of flotation with Malachite green agar (MGA 0.25) and Freeze blotter techniques respectively. In this study, 46 species belonging to 23 different genera were isolated. Cladosporium spp. (57.1–89.2%) and Alternaria spp. (82.4–100%) species were the predominant fungal species identified as endogenous mycoflora. The predominant exogenous fungi were Penicillium spp. (78.4–92.8%) and Aspergillus spp. (71.4–85.7%) species. Fusarium proliferatum was the most prevalent species of Fusarium isolates. Aspergillus niger (39.4%) and Aspergillus flavus (36.7%) were the predominant Aspergillus species identified as exogenous mycoflora. Aspergillus flavus (26.6%) was the predominant Aspergillus species identified as endogenous mycoflora. Flotation method with MGA 0.25 recommended for isolating of hyaline fungi from wheat cereals. In this study one isolate from Fusarium species was isolated on the basis of morphology and ribosomal internal transcribed spacer classified as Fusarium langsethiae but on the basis of partial translation elongation factor-1alpha gene grouped with Fusarium sporotrichioides. To our knowledge, this is the first report about F. cf. langsethiae in Iran and Asia. [ABSTRACT FROM AUTHOR]