A preference in the natural infestation of corn earworm (CEW: Helicoverpa zea Boddie) to specific host genotypes was observed in field trials to assess the pathogenicity of Aspergillus flavus strains in two maize hybrids and inbreds with contrasting levels of resistance to aflatoxin (AF) accumulation. The resistant hybrid (Mp313E × Mp717) had greater than 14-fold infested ears than the susceptible hybrid (GA209 × T173). Similarly, the resistant inbred (CML322) had greater than 7-fold heavier CEW infestation than the susceptible inbred (B73). These two lines with heavy infestation showed delayed silk emergence, in addition to accumulating seed AF levels that are low and sub-toxic to CEW. Since CEW oviposits directly on silks, the availability of green silk for egg-laying in the late flowering genotypes may be one of the contributing factors to their preferential infestation. The level of CEW infestation had little influence on seed AF levels either in uninoculated ears or in ears manually inoculated with toxigenic A. flavus strains. Although no manual inoculation with Fusarium species was carried out, the CEW-infested ears showed a significantly greater seed fumonisin (FUM) content compared to uninfested ears . In spite of its superior resistance FUM accumulation demonstrated previously, Mp313E × Mp717 had greater levels of FUM than GA209 × T173 correlating with the level of CEW infestation. In summary, mycotoxin contamination of crops is determined not only by the level of a host resistance to the cognate fungus, but also phenological traits that compromise its resistance.