The creation of the Yaigojé Apaporis Indigenous Reserve and Natural National Park marked the beginning of a new relationship model between indigenous peoples and the Colombian Government. It was necessary to seek mechanisms to ensure the governance and integral conservation of their life systems, without interfering with their rights to their territorial autonomy and to the cultural management that they have traditionally carried out. Once the park was created, the process of formulating its Special Management Regime (REM) was initiated. This regime was the instrument through which the joint administration of the park was shared by the Colombian Natural National Parks (PNNC) and the Yaigojé Apaporis Indigenous Captains Association (ACIYA). Establishing the REM required an internal (or endogenous) research methodology, proposed by the indigenous communities and supported by the experience of the GAIA Amazonas Foundation. This methodology was based on the guidelines issued by an Amazon Indigenous Congress that identified the topics to be collected in each of the communities, in order to guide the design of the REM. This approach helped promote the participation of indigenous communities with three representatives and a shaman.