The population genetic structure of crop pest populations gives information about their spatial ecology, which helps in designing management strategies. In this paper, we investigated the genetic structure of the Mediterranean Corn Borer (MCB), Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), one of the most important maize pests in the Mediterranean countries, using microsatellite markers for the first time in this species. Insects were collected in twenty-five locations in southwest and southeast France from cultivated and wild host plants (Zea mays, Sorghum halepense and Typha domingensis). Contrary to what has been reported so far in France, we found that MCB populations could be locally abundant on wild poales plants. Analysis was carried out at 11 polymorphic microsatellite markers. Molecular variance was significantly determined by geography, then by host plant, with 17% and 4%, respectively, when considered as a major effect, and with 14% and 1%, respectively, when considered as a marginal effect in permutational analysis. Multidimensional scaling (MDS) and GENELAND Bayesian clustering suggested that populations infecting wild plants (T. domingensis and S. halepense) were more structured locally than those affecting cultivated maize. In S. halepense, significant Isolation By Distance (IBD) indicated that this factor could explain genetic differentiation of the moth populations. In T. domingensis, local population differentiation was strong but did not depend on distance. The implication of this absence of population structure in maize and the heterogeneity of population genetics patterns in wild plants are discussed in the context of the population dynamics hypothesis and population management strategies.