The present investigation was done to evaluate the microbial and fungal contamination and also molecular identification of fungal species in flour, dough and bread samples collected from Isfahan, Iran.Two-hundred and forty different types of cereals including flour, dough and bread were collected. Samples were subjected to microbial and fungal counting and also PCR-based identification of fungal species and sequencing of Aspergillus species. Ranges of total bacterial count of flour, dough and bread samples collected from breads were between 2.83±0.99 and 6.43±1.12 log cfu/g. Flour, dough and bread samples collected from bulk breads had the higher counts of total bacteria than those of flat breads. Ranges of mold count of flour, dough and bread samples collected from breads were between 0.00±0.00 and 1.63±0.63 log cfu/g. Flour, dough and bread samples collected from flat breads had the higher counts of mold than those of bulk breads.Distribution of Penicillium, Cladosporium, Mucor, Aspergillus, Alternaria, Canninghamella, Hyaline, Rhizopus, Epicoccum and Syncephalestrum amongst detected fungal colonies were 24.40%, 20.10%, 20.10%, 19.00%, 3.80%, 3.80%, 3.80%, 2.70%, 1.00% and 1.00%, respectively. Sequencing of isolated Aspergillus genus revealed that all strains were related to flavus, oryzea, terreus,andnijer species. Detected total count and mold count in studied bread samples were lower than limit standards announced by Institute of Standards and Industrial Research of Iran. However, considering the high consumption rate of these kinds of food samples among Iranian people, severe surveillance programs should perform to inhibit from their bacterial and fungal contamination.