Most Skeletonema species have been identified under the name of S. costatum. To assess the morphological species diversity in the genus Skeletonema, we surveyed the nine localities in the coastal waters of South Korea. The light microscopy (LM) and scanning electron microscopy (SEM) observations in this study showed that ultrastructural features of genus Skeletonema discriminated among four species: S. dohrnii Sarno & Kooistra, S. marinoi Sarno & Zingone, S. subsalsum (Cleve) Bethge, and S. tropicum Cleve. In S. dohrnii, cell diameters were 3-6 ${mu}m$ and the pervalvar axes were 13-19 ${mu}m$. One or two partial chloroplasts were visible in a cell. Cells of S. marinoi were 4-10 ${mu}m$ and the pervalvar axes were 8-18 ${mu}m$. Each cell contained one chloroplast. Cells of S. subsalsum which contained 1-2 chloroplasts were 8-13 ${mu}m$ and the pervalvar axes were 11-20 ${mu}m$. Cells of S. tropicum were 10-18 ${mu}m$ and the pervalvar axes were 4-9 ${mu}m$. 2-4 chloroplasts were seen in each cell. Tip width of fultoportula in S. dohrnii and S. marioni was flared and flat, but that in S. subsalsum and S. tropicum was narrow. Morphological groups among them, S. dohrnii and S. marinoi were the most widely distributed in all seasons, while S. tropicum was only occurred in a summer season.