The fate of much of the world’s terrestrial biodiversity is linked to the management of human-modified forest landscapes in the humid tropics. This Special Issue presents the first pan-tropical synthesis of research on the prospects for biodiversity in such systems, with eight individual regional summaries covering Mesoamerica, Amazonia, Atlantic forest of South America, West Africa, Madagascar, Western Ghats, Southeast Asia and Oceania. Two additional papers compare the state of conservation science in tropical forests with both temperate forests and savannah systems. This overview paper provides a comparative analysis of the threats and opportunities facing tropical forest biodiversity, thereby helping to identify the most pressing areas of future research and region-specific factors that contribute towards the effectiveness of individual conservation initiatives. While many of the threats facing tropical forest biodiversity are commonplace they vary markedly in their relative importance across different regions. There is a critical lack of comparable data to understand scale dependent processes, or the relative importance of varying geographic and historical contexts in determining present-day patterns. Conservation science has a key role to play in safeguarding the future of tropical forest biodiversity, but needs to become more effectively embedded in the context of real-world conservation challenges and opportunities. Significant progress can be achieved by improving the cost-effectiveness of research as well as the exchange of ideas and data amongst scientists working in different, often isolated parts of the world. We hope this special issue goes some way top achieving this exchange of knowledge.