Using pollen analysis and metabarcoding of plant sedimentary ancient DNA (sedaDNa), we infer the floristic diversity in the vicinity of Lake Balyktukel, Ulagan Plateau, the Altai Mountains, over the last 7 kyr. The SedaDNA method identified 200% more taxa than found by morphological pollen analysis. In particular, it revealed that the dominant tree for the last 7 kyr was Larix rather than Pinus, which was less frequent in the vicinity of Lake Balyktukel. About 7 ka, larch forest mixed with dwarf birch was widespread on the Ulagan Plateau. The period between 5.3 and 3.4 kyr BP was characterized by the maximal spread of larch forest with an understorey cover of Vaccinium vitis-idaea. Pollen-based annual precipitation reconstruction indicates the most humid phase was between 6.95 and 4.3 ka, and generally coincides with maximal phytodiversity. The most bioproductive period of the lake was from 7 to 6 ka. After that, the trophicity of the lake decreased until 4.5 ka. The appearance of Hippuris vulgaris and increase in Ranunculus subgen. Batrachium at about 5.3–5 ka may indicate the extension of shallow-water ecotopes. Between 3.7 and 3.5 ka, the cyanobacterium Anabaena – an indicator of increased organic matter and algal blooms – was widespread. A planktic thermophilic cladoceran Bosmina longirostris appeared after 1.8 ka and colonized the lake, suggesting an increase in lake trophicity. The last 100 years have been characterized by dramatic changes in the cladoceran community reflecting significant warming of climate.