A new monoraphid diatom species Achnanthidium gladius sp. nov. is described from Indonesia. The description is based on molecular data (18SV4), morphological analysis and comparison with similar species. According to molecular data, Achnanthidium gladius sp. nov. is closely related to Achnanthidium minutissimum. Morphologically, the new species differs from similar species by the absence of a fascia on raphe valve, cell size, and striae density and pattern. The new species is only known from the type locality in Indonesia. Comparison with close related species is given.