A new cymbelloid diatom species from the genus Cymbopleura (Krammer) Krammer is described on the basis of molecular and morphological investigations. Cymbopleura natellia Glushchenko, Kulikovskiy & Kociolek, sp. nov. is, on the basis of results with molecular data, close to C. naviculiformis (Auerswald ex Heiberg) Krammer. The two species differ both by molecular distance and morphological features. Morphologically, C. natellia sp. nov. is compared with several other species in the genus. This work is a pioneer investigation of cymbelloid taxa using molecular tool from Transbaikal area.