Salinity is one of the most important factors globally selecting and structuring microbial assemblages as it acts as a transition barrier between freshwater and marine environments. Such marine-freshwater transitions are relatively rare events and the number of taxa that can thrive in fresh- and saltwater environments simultaneously is limited, mostly because of osmotic and ionic gradients, which require adaptive evolutions at high energetic costs. For a long time, it has been suggested that microbial eukaryotes (protists) have greater difficulties coping with the selective effect of high salinity, resulting in large decreases in the number of species as salinity increases. This thinking has led to the believe that microbial eukaryotes are a poorly represented domain in high salinity environments compared to prokaryotes and mostly restricted to a limited number of groups (preferentially fungi, a few algae and heterotroph flagellates). But, as most information about microbial eukaryote diversity in such environments derives from microscopy and fingerprinting approaches, the true extent of their diversity in these extreme habitats is still obscure. In our projects we analyze microbial eukaryotes of various hypersaline environments (salinity between 4 - 44%) distributed all over the earth.