Urban sprawl has resulted in the permanent presence of large mammal species in urban areas, leading to human–wildlife conflicts. Wild boar Sus scrofa are establishing a permanent presence in many cities in Europe, with the largest German urban population occurring in Berlin. Despite their relatively long-term presence, there is little knowledge of colonization processes, dispersal patterns or connectivity of Berlin's populations, hampering the development of effective management plans. We used 13 microsatellite loci to genotype 387 adult and subadult wild boar from four urban forests, adjacent built-up areas and the surrounding rural forests. We applied genetic clustering algorithms to analyse the population genetic structure of the urban boar. We used approximate Bayesian computation to infer the boar's colonization history of the city. Finally, we used assignment tests to determine the origin of wild boar hunted in the urban built-up areas. The animals in three urban forests formed distinct genetic clusters, with the remaining samples all being assigned to one rural population. One urban cluster was founded by individuals from another urban cluster rather than by rural immigrants. The wild boar that had been harvested within urban built-up areas was predominantly assigned to the rural cluster surrounding the urban area, rather than to one of the urban clusters. Synthesis and applications. Our results are likely to have an immediate impact on management strategies for urban wild board populations in Berlin, because they show that there are not only distinct urban clusters, but also ongoing source–sink dynamics between urban and rural areas. It is therefore essential that the neighbouring Federal States of Berlin and Brandenburg develop common hunting plans to control the wild boar population and reduce conflicts in urban areas.