An increasing number of Canada’s aboriginal communities have sought to govern themselves by preserving, establishing, or re-establishing their own customary indigenous law or “custom codes” for electing or selecting its leaders outside of the electoral regime of Canada’s Indian Act. This chapter reviews leadership selection and governance disputes in these communities, which can become particularly intractable without a means of effective dispute resolution that is universally regarded as legitimate by all parties concerned. Part I of this chapter reviews Canada’s Federal Court jurisprudence regarding these governance disputes, beginning with jurisdictional questions presented by the ambiguous constitutional status of Canada’s aboriginal peoples’ inherent right of self-government, and then analyzing the evolving jurisprudential definition of custom and the issues that arise in ascertaining its “objective” and “subjective” elements. Part II reviews the mechanisms of Canada’s federal administrative state, its compartmentalization of ancillary governance issues and administrative mechanisms that influence these disputes, from the control of Band membership, to the registration of custom codes and election results, to the imposition of third-party management over a community’s finances in the event a long-standing dispute complicates the administration of federal programs in the community concerned. Part III explores the points of intervention by the Canadian federal government, including the range of facilitative and support measures provided up to and including direct unilateral imposition of an electoral regime under the Indian Act, and the implications of these interventions for the communities in question. Part IV takes as a case study the Lubicon Cree of northern Alberta to explore the complications they present for unresolved land claims in Canada, and the paradoxes of non-recognition – when the peoples in question are not formally recognized by the federal government, or the peoples themselves refuse to recognize the legitimacy of the federal government, or acquiesce to the authority of its administration. Part V reviews the extensive Parliamentary record with respect to aboriginal governance law and policy, with particular focus on the inadequacies of the colonialist framework of the Indian Act. The chapter concludes with a summation of the materials discussed, and how they suggest the need for alternative approaches to governance with respect to Canada’s First Nations and aboriginal communities, one more inclusive of indigenous legal traditions and governance practices and less reliant on the Indian Act and its colonialist framework.