Yukon’s Boreal Mountains (Cordillera) has not been significantly transformed by human activity, however continued growth in population and resource development is inevitable. Currently, only 11% is protected with the majority in high-elevation mountains of the southwest. I identified areas of high conservation value for ~290,00 km2 of Yukon’s Boreal Mountains using ecological benchmark conservation planning tools developed by the BEACONs group. Networks of benchmark areas are primarily intact, i.e. without significant human land disturbance, large enough to accommodate natural fire regimes, and representative of regional environmental diversity. I compared multiple scenarios for networks of benchmark areas varying in level of intactness (i.e., 80%, 90%, and 100% of area without human footprint) and total area (covering 15%, 25%, 35%, and 50% of the study area). The best benchmark area networks representing regional environmental variability were <100% intact and covered 35-50% of the study area. While numerous opportunities for large, intact benchmark areas exist, valley bottoms with unique ecosystems are disproportionately impacted by human land disturbance. Thus, a strategy for conserving valley bottom habitats is critical. The priority conservation areas identified can form the foundation of conservation assessments in regional planning alongside other conservation values (e.g. focal wildlife habitats, rare and special elements).