The arctic-boreal treeline ecotone in Siberia is formed by monospecific stands of three species of larch, Larix sibirica, Larix gmelinii and Larix cajanderi. This area is currently under severe climatic pressure, and changes in forest density and extent are expected. Along with this, the respective ranges of the treeline forming species are projected to shift to the Northeast, which is only possible through migration and displacement of existing populations. Fluctuations in forest extent are known to have previously occurred during the Holocene, and investigations of these processes can aid our understanding of the dynamics of larch forests and the factors governing the distribution of the three species. While pollen records of Larix do not achieve a taxonomic resolution below the level of genus, this can be accomplished using genetic markers. We used sedimentary ancient DNA to analyze lake sediment cores spanning most of the Holocene from the southern Taymyr peninsula, where the ranges of L. sibirica and L. gmelinii come together. Changes of the complete vegetation were revealed by DNA metabarcoding and pollen analyses, while diagnostic mitochondrial haplotypes traced the temporal dynamics in distribution of the two closely related larch species. Additionally, we incorporated these two species into our larch population dynamics model LAVESI to understand the influence of competition between these species. Simulations were forced with regional climate series at locations in the vicinity of the sampled lakes. These analyses offer a high degree of resolution and shed light on the complicated ecological processes leading to a change in overall vegetation.