Stored-product moths cause large economic damage in food-processing industries and storage facilities. Control of indoor pests is currently dealt with locally, and control strategies seldom include different mills or cooperative industries in joint efforts to reduce infestations. In colder climates where conditions hinder flight dispersal of stored-product moths, we hypothesize that human transport between mills will facilitate dispersal. Albeit considered intuitive, this hypothesis has so far never been tested. Male moths from three mills (populations) in southern Sweden and Denmark were collected and by using AFLP pair-wise Fst values were calculated. Cluster (population) origins of the genotypes were computed by using a model-based method, STRUCTURE. The results indicate that known transportation of flour between two mills generate genetically more similar populations of the economically important stored-product moth, Ephestia kuehniella (Zell.) (Lepidoptera; Pyralidae), compared to the third mill, with another distribution area, but situated geographically in between the other mills. The STRUCTURE model placed the sampled genotypes to belong to either two or five original populations, with a higher probability of two original populations. The third mill was consistently different from the other two mills independent of the models’ calculated number of populations. Although the study was restricted to three mills and one transportation route, it highlights the possibility that transportation of food products promotes genetic mixing (i.e. dispersal) of insect pest populations. Including cooperating mills in control (or monitor) strategy schemes against stored-product pest insects would therefore be a more effective action rather than to treat each mill separately.