The difficulty in providing straightforward answers to questions underlying ecological interactions lies in the fact that ecological and evolutionary outcomes are the product of a complex of interacting actors, in which individual species are only a small part. The architecture of mutualistic interactions within a community forming a web-like system can be explored using the network approach, which allows one to better describe and elucidate such complexity. Yet a persistent challenge in the analysis of mega-diversified systems, such as those from tropical ecosystems, is the lack of studies encompassing all major higher vertebrate taxa coexisting in conserved habitats, the major goal of this study. Here we delineate the structure of a hyper-diverse tropical system, the continuum of Paranapiacaba in São Paulo state, in Brazil, and evaluate the consequences of the loss of functional roles to the stability of the ecosystem using a network approach based on a concrete scenario of species threat.