Thalassiosira species are an important component of phytoplankton populations in pelagic waters around the islands of Helgoland and Sylt in the German North Sea. This taxonomic study revealed the presence of at least 27 species, 21 at Helgoland and 21 at Sylt. Fifteen species had not been recorded previously for Helgoland (T. aestivalis, T. angulata, T. concaviuscula, T. curviseriata, T. delicatula, T. diporocyclus, T. hendeyi, T. kuschirensis, T. minima, T. minuscula, T. oceanica, T. pacifica, T. proschkinae, T. tealata, T. tenera) and 16 for Sylt (T. aestivalis, T. angulata, T. concaviuscula, T. constricta, T. curviseriata, T. delicatula, T. guillardii, T. hendeyi, T. lundiana, T. mediterranea, T. minima, T. pacifica, T. partheneia, T. punctigera, T. tealata, T. tenera). We provide brief descriptions with illustrations and document the seasonal occurrence of these species at the two stations. We also discuss investigation methods used for different levels of species recognition, namely Utermöhl counts, light microscopical observations of living net-samples as well as scanning electron microscopy of net-samples and isolated cultures. Clonal cultures of some species were established to facilitate the taxonomic investigations and 18S ribosomal DNA sequencing was carried out to complement the morphological studies. A perspective for a routine species-level assessment strategy is given. © 2007 British Phycological Society.