A key issue in global conservation is how biodiversity co-benefits can be incorporated into land use and climate change mitigation activities, particularly those being negotiated under the United Nations to reduce emissions from tropical deforestation and forest degradation^{1, 2}. Protected areas have been the dominant strategy for tropical forest conservation and they have increased substantially in recent decades³. Avoiding deforestation by preserving carbon stored in vegetation between protected areas provides an opportunity to mitigate the effects of land use and climate change on biodiversity by maintaining habitat connectivity across landscapes. Here we use a high-resolution data set of vegetation carbon stock to map corridors traversing areas of highest biomass between protected areas in the tropics. The derived corridors contain 15% of the total unprotected aboveground carbon in the tropical region. A large number of corridors have carbon densities that approach or exceed those of the protected areas they connect, suggesting these are suitable areas for achieving both habitat connectivity and climate change mitigation benefits. To further illustrate how economic and biological information can be used for corridor prioritization on a regional scale, we conducted a multicriteria analysis of corridors in the Legal Amazon, identifying corridors with high carbon, high species richness and endemism, and low economic opportunity costs. We also assessed the vulnerability of corridors to future deforestation threat.