In developing countries, much remains to be done to truly integrate the livelihoods of rural people and biodiversity conservation into land use decision-making and management processes. Yet, research institutions can support informed landscape management decisions by communities, conservation agencies and policy-makers. This can be accomplished by developing methods and instruments that facilitate coherent linkages between stakeholders across various spatial and decisional scales. Researchers need to facilitate equitable participation in the planning processes and provide information on the options that best integrate biodiversity conservation and livelihoods. This chapter aims to analyse how research has contributed to this objective and how it could be designed for future integrative activities at the landscape level. It identifies lessons from case studies that combine biodiversity conservation and livelihood aims in tropical regions and reviews methodological issues relevant to transdisciplinary research. In addition to the critical elements emerging from case studies, the article highlights the crucial role of institutions in helping to bridge the gaps between science, planning, decision-making and effective management. Finally, it describes an approach that two international research organizations are developing to promote the sustainable use of forests and trees and biodiversity conservation in fragmented tropical forest landscapes.