Vanhoeffenus antarcticus was described by Heinrich Heiden from a net sample taken from 385 m depth by the Gauss expedition (First German Antarctic Expedition) while frozen in pack ice near the Antarctic continent in the austral summer of 1902–3. Valves of this peculiar diatom have only ever been observed in preparations from this locality and only using light microscopy, but an electron microscopy study of this taxon has become possible now that some surviving material from the Gauss expedition has been recovered. Our scanning electron microscopy observations show the presence of a radially arranged system of marginal chambers, connected to hollow radial rays and continuing through unusually long processes to the inside of the cell. Another unique characteristic of this taxon is a marginal ring of pillars bearing hooks rising from the valve mantle–valve face boundary, previously interpreted (based on light microscopy) as a ring of T-shaped spines. However, despite the improved understanding of its valve structure, the systematic position of this taxon and its biology remain enigmatic.