The remains of the extinct Merck’s rhinoceros (Stephanorhinus kirchbergensis (Jäger 1839)), well studied in Western Europe, are rare in Russia. However, thanks to the work of a number of researchers, the geography of the finds and the reconstructed range of the species have been significantly expanded. The time of the optimal existence of Merck’s rhinoceros in Yakutia is now recognized as the Middle Pleistocene; the latest finds, dating from the beginning of the late Pleistocene, are known from the southeast of Western Siberia. We provide new radiocarbon dates for the root of a tooth and bone tissue from a previously unstudied lower jaw of the Merck’s rhinoceros from Altai (AltR), whose taxonomic identity we confirm using genomic analysis. Both dates provide an age estimate of around 40 thousand years, which corresponds to the Karginsky time (MIS 3), and are the youngest for the species on the territory of Russia. The pollen spectrum from the soil filling the bone canal characterizes plant communities of open landscapes with forest areas on the upland or in the floodplain, and reflects either local features of the environment or communities of the cold stage within the Karginsky interstadial. A second Merck’s rhinoceros from the Chondon River (ChR), in extreme northeast Yakutia, was determined by previous researchers to have lived either 45–70 thousand years ago or during the beginning of the Middle Pleistocene. Considering what habitats were available in the region, we propose that the ChR could have lived during the last—Kazantsevo—interglacial (MIS 5e) or later. Both finds, AltR and ChR, extend the temporal range of the species existence.