Among acute infectious diseases, cholera gained more attention in Japanese popular culture and among policymakers than any other. Although many facts about cholera's historical existence seem settled, when one looks closely at the medical, biological, and environmental science, several of these facts—especially about the definitions of pandemics, epidemics, and endemicity—become fuzzy. In an attempt to reach a modicum of clarity, this article asks: What biological and environmental conditions allowed cholera to become endemic in nineteenth-century Japan? In answering this question, it makes the case that understanding this disease in history and, more specifically, why it took the course that it did in nineteenth-century Japan requires knowledge of the scientific literature. This claim is part of a broader argument about how understanding the physical world in its concrete manifestations through biological and environmental science is important to understanding human history. It is applicable not only to the history of disease, epidemics, and pandemics but to other fields, including environmental history, the history of technology, and the history of war, as well. This article also questions a number of boundaries: between disciplines, across time and space, and between evidence and assumption in what we consider facts.