Tissue samples from 160 European hedgehogs, Erinaceus europaeus, representing eight small populations from a highly fragmented landscape in Oxfordshire, UK, were screened for polymorphism at six microsatellite loci. Permutation analysis of allelic compositions revealed no evidence for linkage disequilibrium among loci. Genotype proportions within populations and at five loci did not differ from those expected at Hardy–Weinberg equilibrium. However, significant heterozygote deficit and amplification failure of several samples necessitated removal of one locus from the analysis. Mean observed heterozygosity was 0.70. Average RhoST was 0.079 and differed significantly from zero, suggesting restricted gene flow among local populations. Pairwise Nm values and geographical distance were not correlated, indicating that factors other than distance affected dispersal.