In 1924, the South Manchurian Railway Company adopted a system of fingerprint differentiation to regulate the influx of Chinese miners into the Fushun coal mines. From the regulation of miners to criminal differentiation, and later to the creation of a national citizenship, fingerprinting was a key part in the various stages of Japanese intervention in the territory of Manchuria. When Manchukuo was formed in 1932, fingerprint technology was transformed into an administrative tool for effective control of the indigenous populations. However, similar to the fate of other ambitious projects, a national identity founded on a fingerprinting census failed to come to fruition. This article argues how science and technology was never immune from imperialistic and nationalistic interests as seen in the example of fingerprinting where the historical development represented aspirations for scientific development, modernization, as well as political and economic progression. It shall incorporate paradigms in the history of science and technology into current historiography of the Japanese process of empire-building, to reveal how a scientific knowledge, such as fingerprinting, is positioned in the global history of labor discipline and empire-building.