This paper aims to reconnect the history of modern Japan with that of Japan's colonies by examining debates over the legal inclusion and exclusion of colonial Taiwan in 1899. It examines why and how an inconsistent legal structure evolved within the Japanese Empire. I argue that the creation of the Japanese nation was intertwined with the empire, and that this can be seen in the discriminatory deployment of the Family Register and Nationality Laws. Japan included Taiwan within the scope of the Nationality Law to achieve full sovereignty over its territory but also excluded the colonised people of Taiwan from the family register system to deny them citizenship. The rapid reconfiguration of the idea of 'Japan' under the strong influence of the West added significant ambivalence to this process, and thus to the making of the nation-empire.