The present paper analyses the links between Payments for Environmental Services (PES) and biodiversity conservation in developing countries. We first discuss some of the inherent complexities and uncertainties when linking biodiversity to ecosystem services and the related inconsistencies to deal with ecosystem services monitoring, quantification and biodiversity economic valuation. We then apply such theoretical framework in 11 biodiversity PES field projects to evaluate the impacts on biodiversity conservation and rural development. We find that PES designed for conserving ecosystem biodiversity with no concrete species targeting, require less monitoring and payments are done on a per surface basis. Biodiversity PES projects targeting concrete species require more monitoring and control, and payments are done on a per family basis. These projects have not addressed the polemic of the lack of consistent links between ecosystem functions and biodiversity, and have adopted a practical approach where biodiversity depends on land uses or targets specific species threaten by extinction. We finally suggest some design features to better adjust PES to local needs while coping with forthcoming socio-economic challenges.