The Aspergillus flavus population structure from maize kernels was examined. During 2011, samples were collected from two main grain maize production areas in Iran (Fars and Ardebil provinces), shortly before harvest. One-hundred nine A. flavus isolates were recovered on Dichloran Rose Bengal Chloramphenicole (DRBC) agar and Aspergillus flavus/parasiticus medium (AFPA) and grouped into morphotypes and Vegetative Compatibility Groups (VCGs) based on morphological (e.g. sclerotia production), physiological (e.g. aflatoxin-producing ability) and genetic criteria (e.g. heterokaryosis). In general, morphotype and VCG composition were highly dissimilar in both provinces. In total, 43.8% and 44.3% of A. flavus isolates from Ardebil and Fars, respectively, produced sclerotia. Sclerotia producers were identified as A. flavus L and S strain morphotypes in Ardebil (66.7% and 33.3%, respectively) and Fars (29.6% and 70.4%, respectively). Furthermore, 71 isolates (65.1%) were able to produce aflatoxin (Ardebil 40.8%, Fars 59.2%). The aflatoxin values were categorized into four different classes (< 10, 10–100, 100–1,000 and > 1,000 ppb). In total, 51 aflatoxin producing isolates of A. flavus (Ardebil n = 22, Fars n = 29) were assigned into 26 VCGs by complementation of nit auxotrophs on nitrate medium. None of the A. flavus isolates from Ardebil complemented with any isolates from Fars. Genetic diversity of A. flavus isolates was 59.1% and 41.8% for Ardebil and Fars, respectively. The different geographical adaptation and genetic make-up of A. flavus isolates may be due to different climatic conditions, soil types and crop sequences in both maize production areas.

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