Frozen sediments from three cores bored in the permafrost surrounding the El’gygytgyn Impact Crater Lake have been studied for pollen, non-pollen palynomorphs, plant macrofossils and rhizopods. The palynological study of these cores contributes to a higher resolution of time intervals presented in a poor temporal resolution in the lacustrine sediments; namely the Allerød and succeeding periods. Moreover, the permafrost records better reflect local environmental changes, allowing a more reliable reconstruction of the local paleoenvironments. The new data confirm that shrub tundra with dwarf birch, shrub alder and willow dominated the lake surroundings during the Allerød warming. Younger Dryas pollen assemblages reflect abrupt changes to grass-sedge-herb dominated environments reflecting significantly drier and cooler climate. Low shrub tundra with dwarf birch and willow dominate the lake vicinity at the onset of the Holocene. The find of larch seeds indicate its local presence around 11 000 cal yr BP and, thus a northward shift of treeline by about 100 km during the early Holocene thermal optimum. Forest tundra with larch and shrub alder stands grew in the area during the early Holocene. After ca. 3500 cal yr BP similar-to-modern plant communities became common in the lake vicinity.