There is a current debate on microbial diversity between the defenders of the cosmopolitan hypothesis, arguing for high gene flow and low diversity, and the defenders of the endemism hypothesis, conversely arguing for restrictions to gene-flow and high degrees of diversity. These hypotheses are evaluated in this thesis by using environmental sequencing and molecular phylogeny. Three groups of unicellular eukaryotes, representing very different lifestyles, are investigated; the cryptomonads; photosynthetic flagellates, the alveolates; intracellular parasites, and the heterothrophic flagellates of the phylum Telonemia. The level of cross-colonization, i.e gene-flow, between freshwater and marine habitat, and the level of geographic distribution within the marine habitat is used to test the hypotheses. The resulting phylogenies show very little gene-flow between marine and freshwater habitats, a result in congruence with the endemism hypothesis. However, high levels of gene-flow between very distant geographic locations was also observed, contrastingly in congruence with the cosmopolitan hypothesis. This shows that neither hypothesis is able to fully describe diversity and distribution processes among unicellular eukaryotes and that a revision is needed.