In Canada, research with indigenous communities is often conducted within the research hegemony of western institutions. The purpose of this paper is to present an appraisal of a community based participatory research (CBPR) study informed by indigenous qualitative methodologies. The research objective was to understand Mi'kmaw youth mental health. Traditional ideologies of research dominate the structures, processes, and outcomes of indigenous research. Consequently, indigenous communities have called for research which is inclusive of indigenous epistemologies, decolonizing, and transformative. Two indigenous theoretical constructs guided this research: two-eyed seeing, and ethical space. These constructs were enacted in partnership with a Community Advisory Committee (CAC) composed of Mi'kmaw youth and adults. The contributions and challenges of conducting indigenous health research employing the theoretical constructs of two-eyed seeing and ethical space, and the barriers and opportunities of employing CBPR with a Mi'kmaw community are presented. The findings of Mi'kmaw youths' understandings are highlighted to provide a context for the analysis of this research that is inclusive of indigenous epistemologies, decolonizing, and transformative. The methods employed in this research offer an approach to conducting indigenous health research within the confines of the research hegemony of western institutions.