The sound management of Social-Ecological Systems (SESs) requires a deep knowledge of the system and its dynamics, but effective strategies also need to include the perceptions of the local actors. These perceptions are specific and might differ for different actors. In this research, we analyzed the gender and across scales differences in the perception of a SES and unveiled the potential reasons that shape the different actors' understanding. Using structural analysis tools, we analyzed the perceptions of local women, local men, and external stakeholders on the most relevant variables shaping the actual and future sustainable management of a SES. The research was developed in Santiago Comaltepec, an Indigenous community located in the Sierra de Oaxaca (Mexico) that manage their forest under community-based strategies. The gender differences in perception showed the inequalities in agency, voice, and power between women and men. The comparison of the perceptions between community members and external stakeholders showed greater similarities, but still reflected power differences and differences in knowledge and cultural representations. We concluded that sound and resilient SES management need to recognize the gendered and across scales diversity in perception, knowledge, and practices and create bridges and synergies among knowledge systems to shape desirable trajectories.