Picoeukaryotes are protist 3 µm belonging to a wide diversity of taxonomic groups, and they are an important constituent of the ocean microbiota, performing essential ecological roles in marine trophic chains and in nutrient and carbon budgets. Despite this, the true extent of their diversity is currently unknown, and in the last decade molecular surveys have uncovered a substantial number of previously unknown groups from all taxonomic levels. No studies on this group have been done so far on the Red Sea, a unique marine environment characterized by oligotrophic conditions and high irradiance, salinity and water temperature. We sampled the surface waters of a site near the northern Red Sea coast, and analyzed the picoeukaryotic diversity through the construction of PCR clone libraries using the 18S ribosomal gene. The community captured by our library is dominated by three main groups, the alveolates (32%), chlorophytes (32%) and Stramenopiles (20.55%). Members of Radiolaria, Cercozoans and Haptophyta were also found, although in low abundances. Photosynthetic organisms are especially diverse and abundant in the sample, with heterotrophic organism mostly composed by the mostly parasitic novel alveolates and bacterivorous stramenopiles. Novel clades were detected among the Novel Alveolates- II and the photosynthetic stramenopiles taxa, which suggests that they may be part of a number of groups unique to the basin and adapted to the high salinity and temperature conditions. This is the first study done on the Red Sea focusing on the diversity of the complete picoeukaryotic fraction, and provides a stepping stone in the characterization of the picoeukaryotic component of the microbial diversity of the basin.