Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Here we investigate microevolutionary dynamics acting on the genome and the immune genes in particular between and among populations by comparing three allopatric populations of the Green Veined White butterfly, Pieris napi (Linné; Lepidoptera, Pieridae). The dataset consists of three pool-seq libraries.