Citation: Valencia, V., P. West, E. Sterling, L. García-Barrios, and S. Naeem. 2015. The use of farmers' knowledge in coffee agroforestry management: implications for the conservation of tree biodiversity. Ecosphere 6(7):122. http://dx.doi.org/10. 1890/ES14-00428.1Abstract. In agroforestry systems, the survival of shade trees is often the result of farmers' deliberate selection. Therefore, how communities generate knowledge and apply it to resource management practices influence the potential for biodiversity conservation of agroforestry systems. In this study, we investigated the use of knowledge by farmers to manage coffee (Coffea arabica) agroforests and the consequences for the conservation of tree biodiversity and composition of surrounding forests. We interviewed 50 coffee farmers to investigate their shade tree preferences and sources of knowledge of the properties of shade trees and coffee management practices; we also conducted tree inventories in 31 coffee farms and 10 forest sites in La Sepultura Biosphere Reserve in Chiapas, Mexico. Our results showed that farmers are modifying agroforests according to their knowledge and tree preferences, and that the resulting agroforest is lower in tree diversity and dominated by pioneer and farmers' preferred tree species as compared to forests. The principal sources of knowledge of management practices are external sources, such as governmental and non-governmental organizations, whereas the primary source of tree specific knowledge is empirical knowledge. We found that the higher proportion of pioneer trees relative to forest is mostly explained by farmers' tree selection decisions (63%) rather than as a byproduct of management practices (37%) that disturb the soil and open the canopy, altering light penetration and microclimate conditions. Based on interviews and tree inventories, we found that farmers gradually replace canopy trees of neutral and disliked species by preferred species, in particular Inga spp. We found that external sources continue to promote the idea that Inga spp. trees bring significant benefits to coffee production in spite of a lack of scientific evidence to support this claim. This indicates that farmers are receptive to incorporate outside knowledge into their knowledge systems and adapt their resource management practices accordingly. Our findings highlight the importance of disseminating sound and clear scientific information to practitioners who work directly with farming communities to ensure that accurate and up-to-date information is being contributed to local knowledge systems.