New conceptual and material methods characterise the thirty years of scholarship on the history of disease in China from the 1980s to the 2010s. The historical-conceptualist approach to writing the history of disease concepts on their own terms started in the 1980s and informed the history of late imperial epidemiology thereafter. Developments in the new field of paleomicrobiology since the 1990s also allowed an analysis of ancient human DNA (aDNA) to be connected with disease history in novel ways. Human and bacterial DNA became new sources for historical enquiry combined with the range of printed sources from dynastic histories to medical treatises. It first reviews scholarship from the 1980s to 1997 before it examines the naturalist-realist interpretation of the end-of-Ming epidemics as plague, subsequent naturalist-realist critique of this interpretation, and then historical-conceptual perspectives on the end-of-Ming epidemics. Then, it turns to the historical-conceptual scholarship on the history of Chinese medicine from 1997 through the 2010s and the naturalist-realist approach exemplified by the scientific transformations in the history of plague in China since 2011. While previously scholars tended to align on either one or the other side of this conceptual spectrum, now there is a productive cross-fertilisation of both approaches to the history of late imperial epidemiology in China.