Resistance to corn earworm (CEW) (Helicoverpa zea Boddie) has been attributed to high concentrations of C-glycosyl flavones and chlorogenic acid in maize (Zea mays L.) silks. The most common C-glycosyl flavones isolated from maize silks are maysin, apimaysin, and methoxymaysin, which are distinguished by their B-ring substitutions. For a better understanding of the genetic mechanisms underlying the synthesis of these compounds, we conducted a quantitative trait locus (QTL) study with two populations: (Tx501 x NC7A)F2 and (Tx501 x Mp708)F2. For chlorogenic acid, maysin, and methoxymaysin concentration, the major QTL for both populations was located on chromosome 4 near umc1963. For apimaysin, the major QTL in both populations was located at the position of the pr1 locus on chromosome 5. The QTL alleles on chromosome 4 that increased the synthesis of methoxymaysin significantly decreased the synthesis of maysin and chlorogenic acid. This decrease in maysin concentration was four-fold greater than the increase in methoxymaysin. Our results indicate that the QTL on chromosome 4, responsible for the increase in methoxymaysin synthesis, alters the dynamics of both the phenylpropanoid and flavonoid pathways.