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Iron is an essential component for growth and development. Despite relative abundance in the environment, bioavailability of iron is limited due to oxidation by atmospheric oxygen into insoluble ferric iron. Filamentous fungi have developed diverse pathways to uptake and use iron. In the current study, a putative iron utilization gene cluster (IUC) in <i>Aspergillus flavus</i> was identified and characterized. Gene analyses indicate <i>A. flavus</i> may use reductive as well as siderophore-mediated iron uptake and utilization pathways. The ferroxidation and iron permeation process, in which iron transport depends on the coupling of these two activities, mediates the reductive pathway. The IUC identified in this work includes six genes and is located in a highly polymorphic region of the genome. Diversity among <i>A. flavus</i> genotypes is manifested in the structure of the IUC, which ranged from complete deletion to a region disabled by multiple indels. Molecular profiling of <i>A. flavus</i> populations suggests lineage-specific loss of IUC. The observed variation among A. flavus genotypes in iron utilization and the lineage-specific loss of the iron utilization genes in several <i>A. flavus</i> clonal lineages provide insight on evolution of iron acquisition and utilization within <i>Aspergillus</i> section <i>Flavi</i>. The potential divergence in capacity to acquire iron should be taken into account when selecting <i>A. flavus</i> active ingredients for biocontrol in niches where climate change may alter iron availability.