The pink stem borer (Sesamia nonagrioides Lefèvbre) is the most important pest of maize (Zea mays L.) throughout the Mediterranean area. The maize composite EPS12 has been chosen as the base population for a breeding program based on its resistance to pink stem borer, with the main selection criterion being resistance to stem tunneling. Yield was taken as a secondary selection criterion to avoid any unwanted negatively correlated response on this character. The aims of investigation were: (1) to monitor the effects of selection for resistance to pink stem borer on allele frequency at 70 simple sequence repeat (SSR) markers and their impact on the genetic structure of EPS12 and (2) to identify loci at which allelic frequencies changed significantly due to directional selection. Genetic diversity was reduced during the selection process (as expected since random genetic drift as well as selection could reduce genetic variability), but not significantly so. Although the loss of genetic variation was generally consistent with that expected in a model in which random genetic drift acts alone on neutral alleles, the changes observed in the frequency of five alleles were significantly greater than expected. Further, the linear trend of the departure from the random genetic drift model was significant for some allelic versions of two SSR markers, umc1329 and phi076; directional selection was therefore acting on these loci. The significant effect of directional selection on those markers suggests the presence of quantitative trait loci (QTLs) for tunnel length and/or for yield under artificial infestation with Sesamia nonagrioides on the long arm of chromosome 4.