The significance of short-term exchange between populations relative to long-term local selection was evaluated in the Daphnia longispina hybrid complex. In a hierarchical analysis, the genetic structure of D. cucullata, D. hyalina and their interspecific hybrid c x h was studied by allozyme electrophoresis. Two data sets based on the variation at three and nine loci revealed high genetic variation in all populations. Significant genetic differentiation, FST, was found between lakes that are less than 14 km apart. FST between subpopulations was around 0.2 for D. hyalina and D. cucullata averaged over three and nine loci. Selection on hybrid genomes may explain why, in c x h hybrids, only 10 per cent of the total genetic variation found was attributable to differences between populations. FST and genetic distances, Dnej,were compared between pairs of populations from different hierarchical levels. In both data sets, differences were highest between species. Between parent species and hybrids, they were intermediate, and they were lowest within species. A regression of log Nm against log distance was used to test for isolation by distance. Mantel tests showed a highly significant decrease in Nm with distance for populations of D. hyalina in both data sets. A negative trend was also found for populations of D. cucullata and c x h. Thus, in contrast to littoral cladoceran species, the pattern of geographical variation between populations of pelagic species seems to be more strongly influenced by gene flow.