Ancient DNA (aDNA) analyses from archaeological animal remains is well suited to many of the objectives investigated through zooarchaeological analyses. This paper aims at presenting the field of palaeogenomics, particularly in its application to zooarchaeological questions. While it does not seek for exhaustivity, it focuses on practical issues, hoping to promote trans-disciplinary dialogues. The authors begin with a presentation of the nature of aDNA and the main taphonomic pathways leading to its differential preservation. Then the authors offer a brief historical review of the aDNA techniques, from the early discoveries of 1984–1985 to the advent of next generation sequencing and high throughput approaches at the beginning of the 21^st century. The aurhors describe the main challenges of aDNA research in recent years as it needs to adapt to a new range of methods and how the study of animal remains has been impacted. Finally, the authors highlight the main outcomes of the application of aDNA to describe animals and their populations and future lines of research that could be explored.