Environmental DNA (eDNA) obtained from ancient samples such as sediments, ice or water are valuable data sources for a wide range of disciplines in past and present biodiversity and biogeography [1-4]. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years and have become an increasingly powerful tool to investigate wide-ranging topics [5]. However, the ancient environmental metagenomics remains many issues that should be to be addressed relating to ancient DNA (aDNA) such as degraded nature, incomplete reference databases, sensitivity to contamination by modern DNA [6-8]. This review aims to provide an overview of the use of ancient metagenomics in large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes and illustrate the limitations, risks, and potentiality of this ancient eDNA research via high-throughput sequencing (HTS) technologies. Further, paleogenetic and paleogenomics will provide diverse insights into studying evolution and how the present world came to be.