Natural hybridization, the interbreeding of species, can contribute to understanding the processes of maintaining biodiversity. There are different theories to explain the coexistence of hybrids with their parental species. Some models assume that hybrids are temporarily more or equally successful as parental taxa in a specific environment; but even in case of lower fitness of hybrids, a dynamic equilibrium between natural selection against hybrids and dispersal explains the maintenance of hybrid zones. Although the long-term significance of hybridization in animals is poorly understood, it is common among cyclical parthenogens, especially in zooplankton species of the genus Daphnia. In the first part of my thesis (Chapters 2-4), I investigated the population structure of Daphnia longispina assemblages under different selection pressures. First of all, in Chapter 2, I detected a nearly perfect correspondence in the assignment of Daphnia individuals to different parental and hybrid taxa based on microsatellite markers (15 loci) when examining reference clones which had been previously classified by different markers (allozymes, mtDNA). This allowed me to identify species and different hybrid classes from field samples by microsatellite markers alone and their assignment was verified by a set of statistical approaches (Factorial Correspondence Analysis and two Bayesian methods). Secondly, by applying microsatellite markers on Daphnia samples isolated from eight different lakes, I explored the dynamics of the hybridizing system (Chapter 2). Within taxa, replicated genotypes were of clonal origin but clonal lineages rarely persisted in subsequent years suggesting that populations must go through sexual reproduction to be re-established in spring, from sexually produced diapause eggs. In addition, I also observed a complete replacement of taxa between two spring seasons (Chapter 2). Such a year-to-year taxon replacement has not been reported for the D. longispina complex before. I additionally detected that the genotypic diversity is lower in hybrids than in parental species (Chapters 2 and 3), supporting the existence of reproductive incompatibilities between the parental genomes. Thirdly, in order to understand the impact of cyclically parthenogenetic reproduction on populations, I explored the changes in taxon and clonal composition of Daphnia populations, across time (generation-to-generation) and space (between sampling stations), during a period of seasonal environmental change (Chapter 3). I observed that clonal diversity increased with time, as a few dominant clones were replaced by a higher number of less common clones. I assumed that a loss in selective advantage for the dominant clones may have been due to parasite selection acting in a negative frequency-dependent manner. Therefore, in Chapter 4, I investigated the possibility of parasite-mediated selection in D. longispina populations. I found significant differences in clonal composition between random and infected parts of the host population. This suggests that parasite-driven selection might operate in natural Daphnia populations, as parasites influence the clonal structure of host population. In the second part of my thesis (Chapters 5), I investigated how host-parasite interactions could be altered by predation. Specifically, I tested the potential costs of simultaneous prey exposure to enemies from different functional levels (i.e. predators and parasites). I found that the proportion of successful infections and the number of parasite spores were higher among defended (against predators) than undefended Daphnia, demonstrating a previously unknown and environmentally relevant cost to inducible defences. These results enhance our understanding of how epidemiology can be integrated into the concept of phenotypic plasticity.