Climate change challenges traditional strategies to conserve native biological diversity while sustaining ecosystem services. Several key climate adaptation frameworks call for adoption of experimental management whereby different strategies are viewed as experimental treatments requiring untreated controls by which to compare alternative approaches. At the same time, a variety of traditional conservation approaches (e.g., protecting land as connected network of reserves) continue to be emphasized as critical climate adaptation strategies, assuming that reserves are sufficiently representative of ecological diversity. Lands within the National Wilderness Preservation System could be used as untreated control landscapes while also serving as cores within protected area networks. The value of NWPS lands to serve as both untreated controls and representative ecological reserves will require maximizing ecological diversity within protected areas. Here, we assessed ecological representation across wilderness, potential wilderness, and other lands located on the Flathead National Forest (FNF). Our aim was to quantify and map ecological cover types currently underrepresented in wilderness. Underrepresented land cover types included diverse low-elevation mixed-conifer forests. These cover types were well-distributed within potential wilderness, suggesting opportunities to expand untreated controls while diversifying ecological reserves. Investigating the proportion of potential wilderness composed of underrepresented ecosystems provides a means to prioritize areas for future wilderness recommendations. However, on the FNF large potential wilderness areas provide opportunities for significantly increasing the representation of individual ecosystems from minimal representation in wilderness. The method demonstrated here could be used in other national forest planning efforts to prioritize recommended wilderness based on increasing ecosystem representation at national and forest-wide scales.