The specific distribution patterns of microbial eukaryotes raise the question for specific adaptation strategies to cope with different external salt concentrations. While high-salt adaptation strategies have been a focus of prokaryote microbiology for a long time, microbial eukaryotes are a sadly and severely neglected group in this respect. For halophilic prokaryotes, two fundamentally different processes as adaptations to high-salt environments are described: the “salt-in-strategy” involves the intracellular accumulation of molar concentrations of chloride and potassium, whereas the “salt-out-strategy” excludes salts from the cytoplasm while producing high concentrations of organic compatible solutes, which are inert and do not greatly interfere with enzymatic activities. Using transcriptome and genome analyses, as well as mechanistic approaches, we investigate the ecophysiology of halotolerant microeukaryotes, in specific heterotroph ciliates, which exhibit different salt tolerance ranges, to fill this gap in knowledge.