The future of biodiversity depends on actions taken today by a variety of actors working together to overcome the complexity that creates its conservation. Designing and implementing these actions put to the test the ability of such a group of actors from different scientific disciplines and professions to share and build the knowledge that is needed to do so. The success of conservation projects depends to a large extent on the integration of different kinds of knowledge and their underlying epistemologies. This integration characterizes transdisciplinarity. An increasing amount of studies focuses on the difficulties to develop transdisciplinary approaches due to the sub-division and specialization of research disciplines. Little work deals with the difficulties faced by the researchers that are engaged in a mode of knowledge production associating different scientific disciplines and professions. Among these difficulties, the link between the content of science and the values and believes underlying researchers’ and stakeholders’ perspectives remains unexplored although it is a critical point in the success of collaboration. A transdisciplinary project on local seed use in an ecological restoration in the Pyrénées is taken as an example to show how not taking into account such link could lead to the failure of a project. Analyzing this failure revealed that the success of a problem-based project is highly dependent on the compatibility of each partner's thought-style, i.e., epistemological background, values and conception of the world. Since the success of a transdisciplinary project depends on the ability of the partners to collaborate, not only technical and methodological issues should be debated as it is always the case, but also the paradigms underlying the collective action. Overcoming thought-style divergences require the partners to enter into a collective learning process. This learning process deserves a specific task dedicated to a reflexive analysis involving all the project's partners.