Research on ancient pathogens enables us to gain new perspectives on the evolutionary history of pathogens and their adaptation to different host organisms. By integrating the latest ancient DNA methods, historical pandemics can be characterized via the identification of their causative agents in genome-wide studies, which also allow for tracing the history of a pathogen back through time. Here we will explore examples highlighting the different directions in ancient pathogen genomics to showcase current and future perspectives of the field.