This study was developed around concerns about how indigenous knowledges have been represented and applied in environment and development education. The first phase of the study is a genealogical analysis after Michel Foucault. This probes representations and applications of plant-based indigenous knowledge in selected anthropological, botanical and environmental education texts in southern Africa. The emerging insights were deepened using a Social (Critical) Realism vantage point after Margaret Archer to shed light on agential issues in environmental education and development contexts. Here her morphogenetic/morphostatic analysis of social transformation or reproduction is used to trace changes in indigenous knowledge representations and applications over time (from the pre-colonial into the post-colonial era). The second phase uses the same perspectives and tools to extend the analysis of power/knowledge relationships into the interface of indigenous communities and modern institutions in two case study settings in the Eastern Cape of South Africa. This study reveals colonially-derived hegemonic processes of modern/Western scientific institutional representations/interpretations of the knowledges of indigenous communities. It also tracks a continuing trajectory of their dominating and prescriptive mediating control over local knowledges from the pre-colonial context through into the post-colonial period in southern Africa. The analysis reveals how this hegemony is sustained through the deployment of institutional strategies of representation that transform local knowledges into the disciplinary knowledge discourses of modern scientific institutions. These representational strategies therefore generate/reproduce and validate disciplinary discourses about the other, constructing disciplinary 'regimes of truth'. In this way modern institutions appropriate and displace indigenous/local knowledges, silence the voices of local communities and regulate individual and community agency within a continuing subjugation of indigenous knowledges. This study reveals how working within modern institutions and disciplinary knowledges in participative education and development interactions can serve to implicate indigenous researchers in these institutional hegemonic processes. The study also notes evidence of a continued resistance to hegemonic Western knowledge discourses as indigenous communities have sustained many knowledge practices alongside Western knowledge discourses. There is also evidence of a recent emergence of counter-hegemonic indigenous knowledge discourses in environmental education and development practices in southern Africa. It is noted that these have been contingent upon the changing political terrain in southern Africa as this has opened the way for alternative discourses to the dominant conventional Western knowledges in formal education and development contexts. The counterhegemonic discourses invert power/knowledge relations, decentre hegemonic discourses and reposition indigenous knowledges in formal education and development contexts. This study suggests the need to foreground indigenous knowledges as a process of knowledge decolonisation that gives contextual and epistemic relevance to environmental education and development processes. This calls for a need for new strategies to transform existing institutions by creating enabling spaces for the representational inclusion of indigenous knowledges in formal/conventional knowledge discourses and their application in social contexts. This opens up possibilities for plural knowledge representations and for their integrative and reciprocal co-engagement in situated contexts of environmental education and development in southern Africa.