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Conservation conflicts in protected areas are varied and context-specific, but the resulting effects are often similar, leading to important losses for both humans and wildlife. Several methods and approaches have been used to mitigate conservation conflicts, with an increasing emphasis on understanding the human-human dimension of the conflict. In this article, we present a revision of several conservation conflict cases in the management of protected areas, transdisciplinary and participatory approaches to address conservation conflicts, and finalize by illustrating the application of the nominal group technique (NGT) with the case of the human-giant tortoise interactions in Santa Cruz Island, Galapagos. In this article, we demonstrate the use of novel and systematic participatory and deliberative methodology that is able to engage stakeholders in a constructive dialogue to jointly identify and explore options for shared strategies and solutions to conservation conflicts. The results are comparable with other conservation conflicts cases around the world and illustrate the importance of generating legitimatized information that will further help policy and decision-making actions to address conservation conflicts in the management of protected areas.