Overlapping areas between Protected Areas and Indigenous peoples’ territories are important spaces for articulating cross-scale governing institutions and augmenting socioecological adaptability in developing countries. However, cooperation hinges on conflicts resolution between local (Indigenous peoples’ authorities) and national institutions (Protected Areas’ federal managers), official recognition of ancestral rights to Indigenous peoples, and the investment of social and financial capital for protecting important natural resources in synchrony with local communities. For this, is necessary to improve our understanding of the impacts of cross-scale interaction on natural resources’ conservation. In this research, we study these interactions on the Orinoco River watershed, one of the most important areas for the conservation of biodiversity in South America. Overlaps between Protected Areas and Indigenous peoples’ territories in this watershed account for 9% of its surface area. To test the effect of different political setups on conservation, we employed conservation indicators that use spatially-defined biophysical attributes. First, we explored differences between governing units (non-overlapping Protected Areas or PA, non-overlapping Indigenous peoples’ territories or IT, and overlapping areas or OV), then, we analyzed different overlapping categories (Partial, Near, None, and Full), finally, we analyzed how the recognition of ancestral rights impacts local governance by comparing Indigenous territories with rights and without rights. We found that conservation measurements were higher where any type of overlap took place, which suggests that the interaction between local and national institutions has a positive effect on the protection of important ecosystem services, furthermore, the proxies used to measure ecosystem services values indicate that areas contiguous to OV (Near overlapping category) have greater benefit than commonly expected. Our results were inconclusive regarding the effect of public recognition to local authorities on the local governance; however, this study contributes to the body of evidence about the contribution of these communities to the conservation of strategic ecosystems. This research highlights the importance of collaborative work for the conservation of natural resources, furthermore, it could support future investments of public funds on the creation and strengthening of cross-scale alliances and coalitions for the conservation and management of strategic ecosystems in the Orinoco River watershed.