The maintenance of genetic diversity in natural populations is one of the central topics in evolutionary-biological research. Studies using allozyme and DNA-markers have revealed a considerable amount of genetic polymorphism in natural populations of a wide range of organisms. Several hypotheses (spatial and temporal habitat heterogeneity; frequency-dependent selection; neutral variation) have been proposed to explain this phenomenon. Recently it has become clear that a metapopulation structure can be important with respect to the maintenance of genetic diversity in local populations and the development of interpopulation genetic differentiation. Extinction and colonization as well as extensive dispersal between neighboring populations can profoundly alter genotype frequencies and genetic diversity in local populations. So far, no studies have been carried out on the influence of a metapopulation-structure on the genetic diversity of cyclically parthenogenetic zooplankton populations. In this study we want to quantify the genetic diversity in natural zooplankton populations of the species Daphnia longispina s.l., Megafenestra aurita and Polyphemus pediculus. We focus on ponds that belong to two complex systems, each of morethan 20 partly interconnected ponds, ("De Maten", Province of Limburg; "Berlare Broek", Province of Oost-Vlaanderen). We aim at obtaining an integrated view of genetic diversity at the intra- and interpopulation level, based on data concerning neutral markers (allozymes) as well as ecological relevant traits. For the latter, we investigate intra- and interpopulation genetic differentiation in quantitative traits which are known to be related to fitness (life-history traits and phototactic behaviour).