This thesis examines the politics of settler colonialism and indigeneity in Taiwan and Hokkaidō, Japan in the last one hundred and fifty years. I argue that the histories of these two settler colonial formations are inextricably linked due to their shared experience of Japanese imperialism in the first half of the twentieth century. By analyzing a wide range of archival materials such as newspaper accounts, legal texts, and government documents, I first trace the emergence of what I term "settler colonial biopower" in the late nineteenth and early twentieth centuries and its mutations in the immediate postwar period on both islands. This mode of settler colonial power, however, has undergone a significant transformation with the rise of multiculturalism over the last few decades. The second part of this thesis is thus devoted to examining recent shifts in the meanings of indigeneity and the changing contours of settler colonial governance in contemporary Hokkaidō and Taiwan