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Aflatoxin contamination is a major threat to maize production in the southeastern United States. Screening for genetic resistance to aflatoxin has led to the identification of aflatoxin-resistance quantitative trait loci (QTL) in maize inbred lines. However, these QTLs typically span large DNA regions, making identification of actual resistance-associated sequences difficult. In this study, we took the portion of the maize B73 genome at chromosome bin 4.06 (APG v3) containing a 22-Mbp QTL (QTL-4.06) associated with aflatoxin resistance and used it as a reference to identify single-nucleotide polymorphisms (SNPs) and insertion/deletion variants (INDELs) that differ between resistant (Mp313E and Mp715) and susceptible (B73 and Va35) maize inbred lines. Our study provides a rich list of SNPs and INDELs that can be used as markers in the fine-mapping of candidate regions in QTL-4.06 and demonstrates the great potential of resequencing in generating higher-density molecular maps that can be leveraged in molecular breeding-based crop improvement. [ABSTRACT FROM AUTHOR]