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Recent botanical and zoological studies have suggested that the Altai Mountains in southern Siberia are an important refugium of the last glacial biota that used to be widespread across northern Eurasia before the Pleistocene-Holocene transition. To obtain insights into the history of this relict biota, we modelled the spatial distribution of habitats during the Last Glacial Maximum (LGM) in the Russian Altai. We prepared a map of the current vegetation of this area based on the ground-truthed remote sensing data, and modelled the distribution of the current vegetation types using the Random Forest technique with climatic predictors. The models were projected onto the CCSM3 model of the LGM climate for the Russian Altai and interpreted for 72% of its area because the remaining part is supposed to have been glaciated during the LGM. The models projected LGM predominance of desert-steppe across most of the non-glaciated area of the Russian Altai, probably associated with areas of typical steppe, tundra grasslands and some other habitat types, including forest patches in stream valleys. It is likely that during the LGM, these habitats supported the cold-adapted open-landscape biota. In the Holocene, most of the previous grassland area changed into forest or forest-steppe and the Pleistocene biota retreated, with the exception of the Chuya Basin and the Ukok Plateau in the southeast, where the habitat change was very small and desert-steppe and associated vegetation types remained preserved. This refugial area is currently rich in the relict Pleistocene species. A different history was suggested for the precipitation-rich area in the northernmost Altai (north of Lake Teletskoye), where the LGM models suggested occurrence of patches of open forest of Larix sibirica and Pinus sibirica in forest-tundra and forest-steppe landscapes. These forests may have provided the LGM refugium for the temperate forest species that currently occur in this precipitation-rich area. (C) 2015 Elsevier B.V. All rights reserved.