Protists are a highly abundant and diverse group of microorganisms that hold important ecological roles in all aquatic ecosystems. Phototrophic protists are responsible for a large portion of the global primary production, and constitute an important food source for many organisms an every trophic level. Heterotrophic protists have key roles in numerous food chains, e.g. as predators regulating prokaryotic densities, and as parasites imposing a strong influence on host populations. Protistan diversity has increasingly been studied in both marine and freshwater systems, but still the majority of protist taxa remain unknown. In recent years, the improvement of high-throughput sequencing techniques has allowed for a higher sequencing depth than before. This influx of sequence data has provided the opportunity to capture a much more detailed picture of microbial diversity, making it possible to further study their distribution and biogeography. In the present study, the composition and structure of the benthic protist community along a natural salinity gradient (from a marine and a lacustrine system) has been investigated using the Illumina MiSeq sequencing approach. Both rDNA and rRNA were sequenced from sediment samples, in order to obtain an assessment of the metabolically active community, and to relate this to biophysicochemical factors measured in the respective environments. In addition, special emphasize was given to a specific protist parasite group, the X-cell, with intention of detecting its diversity and distribution in these marine and freshwater environments. Generally, a huge diversity of protists was uncovered, displaying several patterns in community composition and structure related to environmental factors. A considerable difference in protist composition was observed between marine and freshwater systems. This was demonstrated to be affected by variation in the salinity concentration. Nevertheless, some protists were found in both saline and freshwater environments, indicating the ability to survive in rather diverse environmental conditions. In this study, the X-cell parasite was detected for the first time in environmental samples and, also for the first time, in a lacustrine/freshwater system. The X-cells found here were noticeably different in the genetic composition of the 18S V4 region compared to earlier observations of the X-cell, suggesting that they might constitute new clades within the X-cell lineage.