The study of ancient DNA (aDNA) is a rapidly evolving field within bioinformatics, offering valuable insights into the genetic diversity, migration, and evolution of past populations. Advances in high-throughput sequencing technologies have enabled the retrieval of genomic-scale data from archaeological and historical specimens, including subfossil remains. Bioinformatics tools are essential for processing this data, addressing challenges posed by the degradation of aDNA and recovering useful genetic and even epigenetic information. Key bioinformatics applications include sequence alignment, phylogenetic analysis, and identifying genetic relationships between extinct and extant species. These studies have broad interdisciplinary implications in fields such as archaeology, anthropology, human genetics, ecology, and evolutionary biology. aDNA research has contributed to understanding ancient diets, domestication processes, and microbiomes, with samples extracted from sediments, ice cores, and other environmental sources. However, challenges remain: aDNA is often fragmented and chemically altered, and a high proportion of sequenced DNA belongs to non-target species. Effective separation and identification of target DNA rely on tools like BLAST, Bowtie2, and BWA, and on microbial databases, despite their limitations. Furthermore, the preservation conditions, such as temperature, significantly affect DNA survival. Fossils like those of mammoths or Aurochs offer valuable material for genetic studies, though phylogenetic isolation, as seen in saber-toothed cats, can hinder comparative analysis. Nevertheless, ongoing technological progress continues to refine the understanding of ancient genomes.