While raccoons (Procyon lotor) cluster into five genetic populations in Germany, the precise spatial extent and degree of overlap of these clusters are unknown. The raccoon roundworm (Baylisacaris procyonis), a parasitic nematode that can cause severe disease in humans, is known to occur in central Germany in two of these five populations. Here we confirm a close alignment between the geographic distribution of the roundworm and the spatial extent of the genetic populations of raccoons in which the parasite occurs. We found little evidence that linear landscape features substantially limit gene flow between populations. Given the large amount of genetic admixture at cluster boundaries, the raccoon roundworm is likely to spread to roundworm-free raccoon populations in the future.