Fungi widely distributed in nature and the study of fungal toxins is important among the research topics. Many of these toxins enter into the body through foods such as flour, bread and other foods. These toxins could lead to complication such as syndromes and cancer in humans. Due to importance of flour over the diet of Iranian people, the incidence of fungal contamination of flour was done in Zahedan bakeries. In this descriptive study, 113 bakeries were randomly selected from different regions in Zahedan. The samples of flour have cultured in order to identify fungal species with specific medium. 34 out of 113 samples had fungal contamination. The most common mycotoxins ÂÂ producing fungi were Acremonium and Aspergillus fumigatus respectively. According to the results of this study and since the bread is the staple of the Iranian people health regulation and monitoring their implementation at all stages of production, distribution and storage of wheat and flour is recommended to the authorities in order to eliminate the fungal contamination and seems to be imperative.