Abstract A new monoraphid diatom species Achnanthidium tinea Tseplik, Kulikovskiy, Kociolek & Maltsev, sp. nov. is described from Indonesia. The species is described on the basis of molecular and morphological analyses. According to molecular data the new species belongs to the clade that includes strains of Achnanthidium minutissimum , Achnanthidium saprophilum and Achnanthidium digitatum . Morphologically, the new species differs quite significantly from other species of the same genus because of linear-elliptic valves with almost parallel sides and strongly radiate striae and a butterfly-shaped fascia on the raphe valve. The morphology and phylogeny of the new species are discussed, and thoughts on the current state of the taxonomy of the genus Achnanthidium are expressed. Our work shows the importance of using molecular data in diatom systematics and also demonstrates the need to investigate rarely studied regions of our planet.