A small marine benthic diatom pertaining to the order Achnanthales (Bacillariophyta) was observed from the Scattered Islands (“Eparses”, Mozambique Channel, Indian Ocean) and from Napuka Atoll (North of the Tuamotu Archipelago, South Pacific). The latter taxon has unique characteristics (e.g., raphe valve striae composed of small areolae versus macroareolae on the sternum valve, low and plain mantle, simply hooked terminal raphe endings, high and complex cingulum composed of plain and open cingular bands, presence of a vestigial raphe) matching none of the genera split from Achnanthidium Kützing sensu lato (e.g., Planothidium Round & Bukhtiyarova, Karayevia Round & Bukhtiyarova ex Round, Psammothidium Bukhtiyarova & Round, Rossithidium Round & Bukhtiyarova), neither the new genus Madinithidium Witkowski, Desrosiers & Riaux-Gobin from which the striae of both valves are composed of macroareolae and the terminal raphe endings are doubly hooked. Pseudachnanthidium megapteropsis sp. nov and gen. nov is proposed. Due to its small size and to the fact that its striation is not discernible using light microscopy, the new taxon probably escaped the attention of taxonomists in the past. This taxon is found along with Madinithidium flexuistriatum that has close but distinctive morphology, clearly marked off under scanning electron microscope (SEM). Observation with a SEM is essential to differentiate the two latter small-celled and elusive taxa that have overlapping ecological niches. It remains unknown whether Pseudachnanthidium megapteropsis is a cosmopolitan-tropical taxon or if its environmental tolerance is wider. Two other small taxa possibly pertain to the same new genus: one from Reunion Island (Mascarene Archipelago, Indian Ocean) and the second from the Scattered Islands (Mozambique Channel).