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Microzooplankton (e.g. ciliates and rotifers) is an important ecosystem compartment responsible for the transfer and recycling of nutrients in pelagic ecosystems. In the Baltic Sea, species diversity of microzooplankton is high. The characteristic feature of the Baltic Sea planktonic fauna is that great part of it is represented by the freshwater species. In comparison with other seas, species composition of the Baltic Sea's ciliates and rotifers have been studied more completely. Now, 789 species of ciliates are known for the Baltic Sea, and only 160 of them are true planktonic. Thus, the need to define better the diversity of planktonic ciliates is essential. In particular, nanociliates (<20 mum) and their functional role in the Baltic pelagic ecosystems are poorly known. Several species of ciliates that are new for the Baltic Sea were discovered by the authors in the Neva Estuary (eastern Baltic Sea). Diversity of rotifers in the Baltic estuarine ecosystems was investigated in more details and accounts to ca. 150 species; meanwhile the species composition of rotifer assemblages in the open Baltic Sea is still in need of revision.