The first part focused on the genetic diversity of foraminifera, with an emphasis on freshwater environments. Four new species of morphologically simple, single-chambered (monothalamous) foraminifera were described and one morphospecies was genetically characterised. To better characterize the environmental diversity of freshwater foraminifera we investigate sediment samples from the Geneva basin, where freshwater foraminifera have been reported a century ago. Phylogenetic analyses suggested that the colonization of freshwater habitats by foraminifera occurred several times during their evolution. At the end of the first part, the results of the single-cell HTS study of intragenomic polymorphism in foraminifera have been presented. This study addressed a common observation that the high sequence diversity revealed by HTS metabarcoding studies is largely superior to the number of morphospecies from the same environment. The second part of this thesis has been focused on the application of HTS metabarcoding to assess the ecological quality of watercourses. We compared the value of the Swiss Diatom Index (DI-CH) inferred by traditional morphological approach to the molecular data generated by HTS.