Aflatoxin contamination of maize (Zea mays L.) grain caused by Aspergillus flavus is a serious health hazard to animals and humans. Resistance to infection by A. flavus is poorly understood. The objectives of this investigation were to identify potential candidate markers associated with resistance in maize kernels and pollen grains to A.flavus. We grew parents [Mp313E (resistant) and SC212m (susceptible)], F1, and F2 plants in the field in 2005 summer. We used a mapping population of 147 F2 plants. Leaf samples were collected for DNA extraction. Fresh viable pollen was collected from individual plants. Each F2 plant was self-pollinated to obtain F3 seed. Selfed seeds from parents, F1, and F2 were challenged with A. flavus conidia and incubated using a medium-free screening technique of Li and Kang. Percent kernels infected and percent pollen germination in presence of A. flavus were recorded. A linkage map was constructed, via Joinmap 4.0, using DNA profiles of all F2 individuals produced from AFLP and Target Region Amplification Polymorphism (TRAP) markers. QTL analysis was performed using MapQTL 3.0 software. One major and one minor QTL were observed for percent kernel infection. Potential markers associated with this trait were also identified via discriminant analysis (DA). Two QTL were detected for log-transformed percent pollen germination via QTL analysis. One of the QTL was associated with a TRAP marker. The DA confirmed the existence of two QTL. The QTL detected for pollen germination were different from those detected for percent kernel infection. Resistance of pollen and of kernels to A. flavus appears to be controlled by different genetic systems/mechanisms. Correlation between pollen germination and percent kernel infection was negligible (r=0.067). Screening of maize populations/inbred lines for markers associated with resistance to both traits should be helpful in developing hybrids possessing resistance to A. flavus.