This paper explores the intersections of Indigenous knowledge management systems and gender in knowledge organization, reflecting on their potential to shape, challenge, and enrich our understanding of identity. We begin by reviewing the ways that Indigenous Knowledge Organization (IKO), knowledge management systems, and queer archival theory are converging in information spaces, before presenting two case studies of knowledge organization that highlight intersectional problems and tensions inherent in attempting to represent complex identities in archival and knowledge management systems. We discuss how two-spirit identities are challenging traditional categories of gender identity in traditional naming conventions. Second, we examine the complexity of Native American boarding schools, the inherent hierarchical structures in knowledge management systems, and the relational systems that can be used to create more inclusive and responsive knowledge structures. We explore how archival knowledge management systems can be made more relational, using the examples within the digital tool Social Networks and Archival Context (SNAC), and the challenges of relying solely on written structures to verify embodied knowledge and gender identity. We consider practical interventions to modify knowledge systems into being more adaptable, and the tension between deconstructing and building upon existing knowledge structures, using queering metadata as an example.