We analyze institutional challenges for a joint transboundary protected area regime. Employing the case of Mt Elgon in Uganda and Kenya, we use the concepts of fit and interplay to guide our examination in the challenges of the establishment of a transboundary protected area management (TBPAM) regime. Although transboundary regimes are thought to provide better fit for the resources, fitness is a contested phenomenon. The findings are critical to the perceived benefits of the TBPAM strategy in the form of one, fully integrated regional regime. We reveal how such a regime will be seriously constrained by the interplay of complex institutional factors. We moreover find evidence that TBPAM entails a reintroduction of the old top-down conservation paradigms, counteracting the community conservation attempts. Therefore, policy makers are encouraged to approach critically the daunting exercise of a continuum of TBPAM governance toward fully integrated management within a joint TBPAM regime. Instead, the focus should be on identifying the issues that are truly transboundary in nature and construct governance structures that directly address these. In this paper we suggest that policy makers carry out a clear institutional analysis: disaggregate the real transboundary objects, identify common interests, and look for appropriate content and levels of cooperation. It is no panacea to establish an integrated transboundary regime, even if two protected areas happen to be adjoining.