In this paper, we introduce a research project aimed at methodological and computer-based support for participatory management of protected areas, in order to promote biodiversity conservation and social inclusion. Our starting point is the “companion modelling” approach, as defined by the ComMod group, a movement of researchers created in 2003. Their method, called MAS/RPG, consists in iterations coupling role-playing games (RPG) and agent-based simulations (MAS), in order to model collective management and support negotiation between stakeholders. It has been applied to the collective management of natural renewable resources. The agent-based simulations are used to foresee, display and discuss the impact of individual actions on the environment. For obvious reasons, companion modelling does not provide stakeholders with a pre-defined solution to their conflicts. More recently, an evolution of the MAS/RPG approach named “agent-based participatory simulations” proved able to prompt participants to create innovative distributed solutions to complex problems. These simulations rely more heavily on computer support (distribution, logs, assistant agents) and integrate the agent-based simulation with the role-playing game, thus reducing the need for iterations. Our objective is to propose and evaluate the use of this methodology and the associated software tools on different national parks for conservation of natural resources in Brazil. Our first case study is the Tijuca National Park, in Rio de Janeiro. It is inserted in the urban net of a great metropolis (Rio de Janeiro) and suffers from different kinds of human pressure and their impacts, e.g., illegal occupation, water contamination and social tension. This case study addresses the question of conflict resolution, one of the key questions for the participatory management of protected areas.