Three rare Psammothidium species were found in recently surveyed lakes of Northeastern Siberia, Russia. One of these species found in lakes of the Kolyma Lowland, is new for science and is formally described here as Psammothidium onufrii sp. nov. It is morphologically similar to the brackish–water species Achnanthes punctulata, but it lacks a central area on rapheless valve and possesses a large central area on the raphe valve. Psammothidium onufrii is characteristic for tundra thermokarst lakes with moderate mineral content. Psammothidium sacculum previously reported from a few subarctic and arctic locations was found in several lakes of the Kolyma Lowland and of the Magadan District. The frustule ultrastructure of this species is documented for the first time here. The third species, known as Achnanthes obliqua (W. Gregory) Hustedt and transferred here to Psammothidium, is a morphologically distinct and relatively rare diatom occasionally reported from northern regions of Eurasia and Western North America. In Northeastern Siberia it was found in sediments of relatively large shallow lakes with low to moderate mineral content. Detailed morphological characterization of the three Psammothidium species will facilitate their detection in environmental surveys and their use in paleoenvironmental reconstructions.