Skeletonema costatum like cells are recorded globally and often generate a huge biomass when blooming. In the present study we performed a taxonomic and geographic survey of the species diversity in Skeletonema along the Chinese coastline. We concentrated our efforts on Xiamen Harbour, where we followed the annual cycle of the generic diversity by collecting 51 water samples from 2006 to 2010. A total of 687 strains of Skeletonema were established and they were identified as S. ardens, S. costatum, S. dohrnii, S. grevillei, S. menzelii, and S. tropicum. S. dohrnii is a winter-spring species, whereas other species tend to appear in summer and autumn. S. costatum is the single species present throughout the year. To assess how the species overcome the period in which they are not detectable in the water column we also sampled the surface sediments and either isolated resting stages and incubated them into cultures, or we generated monoclonal strains by incubating the sediment and isolated whatever emerged from it. The above six species except S. grevillei, and S. pseudocostatum as well, were detected this way, implying that the species produce resting stages. Resting cells of S. costatum and S. tropicum were actually observed in the sediment.