Microbial eukaryote diversity was assessed in Arctic Kongsfjorden (Svalbard), by constructing SSU rDNA clone libraries. Samples were collected from different depths at the outer basin in summer (2006), plus an additional one glacial and one sediment sample. The libraries displayed diversity based on 284 full-length sequences. Four main phyla as Alveolates, Stramenopiles, Cercozoans, and Metazoans were often screened in this fjord. Alveolate occupied highest percentage of taxa in the library of surface sea water, besides the Metazoan related clones. Moreover, dinoflagellates, diatoms and pico-Prasinophytes were detected as prevalent phytoplankton through the analysis of libraries. Questions related to the quantity of these phytoplankton and their roles in the microbial food loop arose from an ecological viewpoint.