Aim: This paper has three aims: (1) to reconstruct the population history of a flightless silvicolous (forest) ground beetle in a region where strong anthropogenic activity has altered the connectivity of the landscape; (2) to estimate the effects of both contemporary and historical landscape structure on the genetics of populations; and (3) to investigate the reasons for clinal variation in one gene locus found in an earlier study carried out in the same geographical location. Location: Münster (Westphalia), north-west Germany. Methods: We investigated 26 populations of the ground beetle Carabus auronitens Fabricius, 1792 by analysing seven polymorphic microsatellite loci and an allozyme locus. Samples of at least 16 individuals per site were studied. These were obtained from dry pitfall traps placed at 23 sites and from three additional (refuge) populations. We used regression and correlation analyses to investigate the effects of both historical and contemporary landscape structure on the allele frequency distributions of the investigated loci. Spatial autocorrelation analysis was used to study possible clinal variations, and admixture rates were calculated in order to assess the genetic influence of populations from possible refuges. Possible reasons for the development of the cline were examined using simulation models. Results: The allele frequency distributions at the investigated loci could not be explained by selection or isolation by distance. We found clinal variation in 50% of the investigated loci and our simulations indicated that this was unlikely to have developed by chance. Admixture rates show significant influences of the investigated refuge populations on the populations under study. Main conclusions: The findings strongly suggest that the clinal variation is secondary. It results from recolonization of the area by C. auronitens from multiple refuges after anthropogenic landscape changes caused forest fragmentation and led to species isolation.