This chapter traces the emergence of ethnic cleavages in the Indonesian archipelago, across three time periods: (1) the early modern period, (2) Dutch rule and Japanese occupation (1596–1945), and (3) Soekarno’s regime (1945–1966). It shows that although Indonesians have been accustomed to diversity along various dimensions over the years, ethnicity became relevant as a basis for mobilization when the ruling authorities allocated resources and treated groups differently along ethnic lines. At times, ethnic groups engaged in violence to challenge their treatment by existing authorities. These precedents for using violence to contest existing political configurations and to renegotiate the boundaries of who is “in” or “out” set the stage for the more recent mobilizations of violence during Indonesia’s democratic transition.