The overall taxonomic and functional diversity of free-living microorganisms is a major, unsolved question in biology. Over the last decades, a heated debate has taken place over the existence or not of biogeographical patterns (i.e. including local endemism) among protists and micro-organisms in general. Researchers have accumulated evidence for both views, but no general consensus applicable to all bacteria, archaea, protists, fungi and micro-metazoa have yet emerged. Several factors potentially influence the dispersal and colonisation potential of organisms, including life history traits, ecological niche, evolutionary history, as well as the taxonomical level investigated. However, to date, most studies have aimed mainly at defending cosmopolitanism versus endemism, focusing on a limited number of examples and rarely trying to explain the observed distribution patterns. These studies are however often undermined by 1) poor taxonomy, 2) the existence of cryptic taxa within apparently well-defined morphospecies, and 3) geographically imbalanced or otherwise biased sampling.We aim to determine the influence of 1) biogeography, 2) environmental filters, and 3) species traits related to dispersal and colonisation ability such as life history traits, growth rate, size and ecological tolerance on distribution patterns of micro-eukaryotes at different taxonomic resolution. We will focus on Sphagnum mosses as a particular habitat, characterised by high moisture, low nutrients and low pH, in order to minimise the effects of environmental filters. Communities living in Sphagnum mosses are indeed very distinctive from those of other freshwater and soil environments owing to the specific micro-environmental conditions. Sphagnum covers huge surfaces of fens and bogs in the cold parts of the Northern and Southern Hemisphere, and can also be found in higher altitudes in temperate and tropical ecosystems where its distribution is patchy. Sphagnum therefore constitutes a good model for studying “island biogeography” within continents.As a working hypothesis, we postulate that free-living protists vary from very narrow endemics to true cosmopolitans. In task 1, we will identify some of the most extreme cases found in general eukaryotic surveys with a metabarcoding approach, by focussing on different taxonomic levels from infra-specific to generic. As our approach will not be dependent on observation and culture of strains, our analyses will not be flawed by inaccurate taxonomy. In addition, we plan to use massive sequencing protocols that will enable us to multiply sampling points and also to get a complete picture of the diversity of each analysed sample. As many free-living protists spread through metabolically inactive propagules, also called cysts, we will compare the metabolically active part of the communities with the inactive part by evaluating the difference between DNA and RNA diversity, the latter representing the community that can potentially develop when environmental conditions become favourable to the different organisms referred to here as “silent diversity”; This will constitute task 2. And, finally, in task 3, we will identify morphologically and characterise the biological traits of cosmopolitan taxa, such as propagule size, growth dynamics and ecological preferences to get a supplementary insight into the prerequisites for a protist to be cosmopolitan.This research will contribute towards three important broader goals to: 1) revise the global estimates of free-living microorganisms, 2) evaluate the existence of locally endemic microorganisms, some of which may possibly be threatened, and 3) to better predict invasion risks by toxic or pathogenic protists.