Using allozyme data based on four polymorphic enzyme loci, we present an analysis of genetic differentiation among eight Daphnia magna populations, separated by less than 100 m to more than 500 km from each other. In spite of the large range of geographic distances, there was only a slight tendency for an increase in genetic differentiation with increasing geographic distance between populations, and the relation was not significant. This was mainly due to the fact that neighbouring populations were already highly genetically differentiated. Our results suggest that in populations in which only a few abundant clones are present after a period of strong clonal selection, among-populational genetic differentiation as revealed by allozyme markers is inflated as a result of stochasticity involving chance associations of alleles with specific abundant genotypes. Indices quantifying genetic differentiation were much higher among populations with a low clonal diversity than among populations with a high clonal diversity.