This article discusses the consequences and challenges for protected area research resulting from the changes and diversifications of the idea of area protection. The article provides an overview of the diverse types of protected area research and a critical analysis of the potentials and limits of newly emerging forms of research, such as involving stakeholders. The main question raised is to what extent protected area research can be conceptualized in a transdisciplinary way. A short introduction to the discourse on transdisciplinarity will be followed by an analysis of possibilities for conceptualizing protected area research in a transdisciplinary mode. It will be shown that the full potential of the newly emerging form of research can be tapped by orienting protected area research towards different target horizons and by strengthening the embeddedness of protected areas in society.