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Crustacean community structure and dynamics are very well studied in lakes, rivers and oceanic systems but wetlands, where moisture conditions fluctuate, have not received equal attention in research. For example, cladoceran communities in peatland systems in the subarctic region have not been fully investigated. We used paleolimnological and paleoecological methods to study plant and cladoceran assemblages and the community dynamics in two subarctic peatlands, which differ in their hydrological characteristics. At the first site, Iitto, river floods introduce planktonic species to fen pools and the steep topography of the catchment induces rapid but relatively short flooding periods. Fluctuating environmental conditions result in a high amount of cladoceran resting stages in the samples. At the other site, Kaamanen, the cladoceran assemblage goes through clear directional changes, which could be attributed to changes in fen hydrology and ultimately to climatic changes during the past two millennia.