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Background and aims – Two unknown benthic diatom species belonging to the genus Achnanthidium Kütz., and found in French and Nepalese freshwater habitats, were investigated. Both species are here described as new and compared with the original material of Achnanthes minutissima var. macrocephala Hust. [≡ Achnanthidium macrocephalum (Hust.) Round & Bukht.] from Indonesia.Methods – The morphology of three small and capitate Achnanthidium species was investigated using light microscopy (LM) and scanning electron microscopy (SEM).Key results – Achnanthidium coxianum sp. nov. (from the Himalaya) belongs to the group of species with hooked terminal raphe endings, while Achnanthidium peetersianum sp. nov. (from France) has variable terminal raphe endings which are usually slightly bent. Achnanthidium macrocephalum is a much rarer species and illustrations concerning its identity in the literature do not conform to the type studied here.Conclusions – The three species are similar in LM but clearly distinct in SEM. The shape of the areolae and terminal raphe endings separate the species. Achnanthidium macrocephalum has often been misidentified in studies from many areas of the world. It is similar to the new species in valve outline and in its small dimensions.