Disease ecologists strive to understand the causes and consequences of parasite infection, including the emergence, spread, persistence and evolution of infectious disease. These processes can be illuminated by parasite genetic markers, which can be used to track parasite spread and infer population history. Recently, a growing number of studies have used molecular tools to examine questions on the ecology of infectious diseases. We review this burgeoning area of research by focusing on three topics where genetic tools will increasingly make major contributions: inferring parasite transmission, reconstructing epidemiological history and identifying physical and environmental drivers of disease spread. We also discuss areas for future research and highlight the promise of multidisciplinary collaborations among geneticists, ecologists and epidemiologists.