This thesis aims to further develop the methodology of using shotgun metagenomics as means to analyse ancient environmental DNA (aeDNA) and expand its usage in more extensive environments. In addition to elucidating paleo-ecological diversity, efforts have been made to improve reference database coverage; increase data uniformity; quantify species; and further improve the sensitivity and specificity of the taxonomic classification at the species level as well as on subspecies level. Specifically the following objectives have been achieved. (i) A new lowest common ancestor (LCA) inference toolkit (ngsLCA) has been developed to solve one of the current bioinformatics shortages of eDNA metagenomics (Paper 1). (ii) Optimization of the current DNA extraction and purification protocols has been made to improve the isolation of DNA from sedimentary samples. (iii) Direct comparisons of obtained shotgun metagenomes to the more widely used metabarcoding technique, with multiple tests we showing that shotgun metagenomes outperform the metabarcoding technique. (iv) The construction of a plant genomic database and evaluation of effects of this improved reference database on metagenomics-based taxa identifications. (v) A new method has been developed to investigate haplotypes of particular species directly through aeDNA shotgun metagenomics. (vi) Reconstruction of the macroecological evolutionary history of the circumpolar in last 50 thousand years (ii to vi are comprised in Paper 2). (vii) Reconstruction of the floristic history on one of the most remote island covering past 500 years, and based on this the effects of human activities on vegetation was tested (Paper 3). (viii) Attempts have also been made to reconstruct the floristic history of New Zealand (NZ), however the specificity of the taxonomic classification limited by the insufficiency of genetic references from NZ plants (Paper 4). Appending this thesis is a review paper that summarizes the most recent literature and state-of-the-art techniques in ancient biomolecular research, to which I co-authored into the environmental DNA section. Although this was not my main focus, it provides an overall introduction to the field and is therefore appended.