Paleoenvironmental reconstructions help us to track vegetation responses to climatic changes, and can also tell us about the origin of plant organic matter stored in permafrost soils. Siberian permafrost soils are natural archives that preserve DNA over thousands of years owing to long-term cold conditions. This makes them particularly suitable for ancient DNA analyses, which we use to reconstruct past flora at high temporal detail, even for poorly preserved or meager plant macrofossils. We reconstructed Late Quaternary vegetation history from permafrost sediments at the western coast of the Bour Khaya peninsula, previously part of Western Beringia, using sedimentary ancient DNA. Bour Khaya is located within the Late Pleistocene Ice Complex, where fine-grained, ice-rich deposits can be found (Yedoma). Analyses were conducted on an 18.9 m long core drilled from the top of a Yedoma hill (71.420° N, 132.111° E) in April 2012. The core was divided into two parts by a Late Pleistocene ice-wedge, whereby the top of the core included the transition from the Late Pleistocene to the Early Holocene and the part below the ice-wedge was deposited more than 46 thousand years ago, before the Last Glacial Maximum (LGM). Plant remains were sparsely distributed through the core and mainly composed of fine rootlets, small woody pieces and very few seeds and fruits. We isolated total DNA of 54 frozen sediment samples (excluding the ice-wedge) and obtained data on past plant assemblages by DNA metabarcoding. The paleogenetic approach allowed us to detect at least 150 taxa. More than 35 taxa were identified to species level, including graminoids, shrubs, herbs and cryptogams. More than 55 taxa were assigned to genus level and at least 40 taxa were assigned to a level between genus and family. The two parts of the core exhibited several plant community changes through time. Holocene and Late Glacial deposits were dominated by taxa typically present in subarctic moist dwarf-shrub tundra, such as Eriophorum, Ranunculus, Salix and Betula. Deposits dated to the pre-LGM were characterized by the complete absence of Betula and could be subdivided into two parts. The major part below the ice-wedge was dominated by aquatic and wetland taxa such as Potamogetonaceae, Caltha palustris and Eriophorum, but still exhibited a high floristic diversity with the occurrence of Rumex, Pedicularis and Castilleja, a hemiparasitic plant. The deepest parts of the core were dominated by Festuca, Plantago, Potentilla and Puccinellia while aquatic and wetland taxa were almost completely absent. Our results suggest that changes in Western Beringian flora occurred during the Late Glacial leading to a large reduction of the flora but also to the arrival of several subarctic taxa. Ancient DNA metabarcoding proved to be an appropriate tool to investigate Late Quaternary vegetation history, especially when plant macrofossils are rare.