Acting to demarcate the spatial limits of decision-making processes, socio-political boundaries are an inevitable part of a human-dominated world. Rarely coincident with ecological boundaries, and thus having no ecological functional role by themselves, they nevertheless impose substantial costs on biodiversity and ecosystem conservation by fragmenting ownership, governance, and management. Where boundaries are in place, a lack of coordination on either side of a boundary affects the efficiency and efficacy of ecosystem management. We suggest four research pathways which will enhance our ability to address the adverse effects of socio-political borders on conservation: (i) scale-matching, (ii) quantification of the mutual economic benefits of conservation across boundaries, (iii) determining transboundary societal values, and (iv) acknowledging the importance of stakeholder behaviour and incentives.