This study presents the long-term forest history in the forest–tundra ecotone of the Low Yenisei River basin. The new high-resolution pollen and macroscopic charcoal data were inferred from the 8.6 m long peat archive covering the last 6300 years. Climate reconstructions are based on the application of the best modern analogue technique using pollen data. Our findings suggest an alternation of phases of middle-taiga forests of Larix sibirica, Abies sibirica, Picea obovata, and Pinus sibirica (intervals of climate warming: 6320–6050, 5790–5370, 4480–4220, and 3600–2700 cal yr BP, respectively) and open larch woodlands with the participation of Betula, Picea, and Pinus sibirica, typical for northern taiga (intervals of climate cooling and increasing humidification: 5370–4480, 4220–3600 cal yr BP, respectively). The vegetation pattern of the region became similar to the modern one around 2700 cal yr BP. Climate warming caused a northward shift of vegetation-zone boundaries in Yenisei Siberia and an expansion of the range of Abies sibirica by about 200 km to the north compared to the present day. The increased frequency of fires and biomass burning during warm periods may promote the melting of the local permafrost, thereby enhancing the tree growth and regeneration.