Species differ in their life cycle, habitat demands and dispersal capacity. Consequently different species or species groups may respond differently to restoration measures. To evaluate effects of restoration measures in raised bog remnants on aquatic microinvertebrates, species assemblages of Rotifera and microcrustaceans were sampled in 10 rewetted and 10 non-rewetted sites, situated in 7 Dutch raised bog remnants. A total of 129 species (Rotifera 108, Cladocera 15, Copepoda 6 species) were found. The species assemblages, total numbers of species and numbers of characteristic raised bog species did not differ between the 10 rewetted and 10 non-rewetted sites. The dominant pattern in the variation in microinvertebrate assemblages could be explained by the presence or absence of open water and variation in physico-chemical variables of surface water and organic matter. Furthermore, the species assemblages of water bodies situated in the same area were on average more similar to each other than to assemblages from other areas. These differences between areas may be due to differences in environmental conditions of water bodies, and possibly also to differences in the local species pool and the subsequent immigration sequence of species. We conclude that, in contrast to earlier findings on aquatic macroinvertebrates, populations of microinvertebrate species, including characteristic species, can either persist in the raised bog remnants during the process of rewetting or (re-)establish within a relatively short period of time (less than about 5 years).