Biodiversity conservation continues to be a challenging task for societies worldwide. We undertook a resilience assessment to address the following question: What are the ramifications of social-ecological system dynamics for biodiversity governance of a nationally significant landscape? Resilience assessment offers promise for guiding response strategies, potentially enabling consideration of ecological, social, economic, and governance influences on biodiversity-related activities. Most resilience assessments have, however, struggled to effectively incorporate governance influences. We applied a modified version of the Resilience Alliance workbook approach to explicitly address governance influences at each stage of an assessment of internationally significant biodiversity features in protected areas of the Australian Alps. The vulnerability of the Alps system to climate change suggests that it is moving into a release stage, with subsequent transformation hypothesized. Network governance is argued as enabling flexible, adaptive management and comprehensive engagement of stakeholders, both of which are critical to shaping how this transformation of the Alps as a valued focal system will occur. The Australian Alps Liaison Committee provides a promising governance structure for collaboration and comanagement across multiple jurisdictions. Our contribution was to demonstrate how a resilience assessment that explicitly embeds governance influences in social-ecological system dynamics can point to pathways for governance reform in the context of system transformation.