The COVID-19 pandemic presents opportunities and challenges for historians working on the global history of health and disease. This article argues that the history of disease will benefit from interdisciplinary work that brings together historians, microbiologists, and archaeologists. Genomes are historical archives, in two complementary ways. Palaeogenomics provide direct access to genomes of the past, while phylogenetics furnish historical insight from evolutionary relationships. Both palaeogenomics and phylogenetics have already contributed enormously to the history of disease, helping us understand how human ecological transformation drives the evolution of our microparasites.