Examination of material obtained from the Urdaibai estuary (North Spain) during a 2 year phytoplankton sampling programme revealed a rare species of the genus Chaetoceros, C. salsugineus Takano. The morphology of this small (4.0×5.5 μm) member of the subgenus Hyalochaetae has been described using both light and electron microscopy. Regarding the original material, two new features have been observed: longer chains up to 24 cells and a new type of aperture, bisected by the fusion of central protuberances of adjacent valves. This bloom-forming diatom reached high densities in the poly-euhaline zone of the estuary closely related with high temperatures, denoting its neritic and summer preferences. Maximal cell densities (106–107 cells l−1) were reached in August and September when the water column was completely mixed and the salinity and temperature were about 31 psu and 20 °C, respectively. This is the first report of C. salsugineus in Europe and contributes to the knowledge of the morphological and ecological features of this species. Relationships with other small species of the subgenus Hyalochaetae are also discussed.