Nephroselmis clavistella D. G. Faria et S. Suda sp. nov. is collected from coastal sand samples from the eastern and western coasts of Okinawa-jima Island, Japan. The description of the cultured strains is based on light and electron microscopic observations. The cultured strains are phylogenetically analyzed based on 18S rDNA sequences. The cells are remarkably right–left flattened and appear round or ellipse when viewed from their right or left side, and are ∼5.0 μm in diameter. The posterior flagellum curved around the cell body at rest. A single, parietal, crescent chloroplast is yellowish green and contains one conspicuous eyespot in its anterior-ventral edge near the short flagellum base. A pyrenoid with one starch sheath is located dorsal of the chloroplast. The cells are divided by transverse binary cell division, as is common in other species of this genus. The cell body is covered with five types of scales, and among them four scale types are similar to Nephroselmis rotunda. The fifth scale type is a distinctive spiny and club-shaped stellate scale with 10 spines, four of the 10 spines extended ∼150 nm and each are slightly curved with a hook at the end, whereas six spines are club-shaped blunt ended. This scale morphology, an important taxonomic characteristic, has never been described before for the genus Nephroselmis. The cell’s morphology is distinctive from previously described Nephroselmis species, and its unique scale characteristics led us to name this newly proposed species “clavistella,” meaning club star.