Genetic subdivision in local populations of the European house mice, Mus musculus domesticus and M. m. musculus, was analysed to study patterns of gene flow. The data consisted of frequencies of microsatellite alleles in 16 samples (250 individuals) from a total of 11 sites in Jutland, which included successive samples from three sites. Sequences of the control region of mitochondrial DNA in three successive samples from one site were also analysed. Microsatellite genotype frequencies within samples were close to Hardy-Weinberg expectations. Levels of microsatellite differentiation among samples (θ= 0.05–0.21) corresponded to limited gene flow at migration-drift equilibrium (Nm= 1–5). Weak isolation by distance for microsatellites in M. m. musculus suggested that gene flow tends to occur among neighbouring sites. Estimates of effective population size over a few generations were much lower than those corresponding to the long periods needed for arrival at mutation-drift equilibrium. This suggested that subpopulations had been influenced by gene flow since formation, or had originated recently from genetically diverse founders.