Biological conservation is most effective when limited resources can be directed towards the species, habitats, and environmental processes of greatest need. Rare ecosystems, which support unique assemblages of specialized and/or diverse flora and fauna within a small geographic area or restricted range often represent vulnerable elements of biodiversity. Here we provide the first formal recognition of Alaska’s rare ecosystems. Thirty-four ecosystems, representing different levels of biological organization (plant associations and biophysical settings) and geographic scale are described, mapped, and assessed with respect to conservation need and current level of protection. While most (>70%) rare ecosystems have low conservation need or are largely managed for biodiversity, these designations are inconsistently aligned; imperiled systems are not necessarily well-protected and fully-protected systems are not necessarily imperiled. Furthermore, it is unclear if the minimum level of protection adopted herein (40% of an ecosystem’s distribution managed for biodiversity) will be sufficient for the conservation of a given system in Alaska. The documentation of rare ecosystems across mid-levels of biological organization and multiple geographic scales presented here complements both species- and landscape-scale conservation assessments previously completed for Alaska. Collectively, these assessments provide a comprehensive and thus precautionary approach to bioconservation in Alaska, specifically one that could build capacity for ecosystems to accommodate the growing impacts of climate change.