There is significant debate about restoration targets for ponderosa pine (Pinus ponderosa) and mixed-conifer forests in the Sierra Nevada, California, USA. On one side are recommendations to create both extensive open and park-like pine forests, and to reduce high-severity fire occurrence by mechanical thinning of forests. These recommendations drive current management. On the other side are recommendations to manage landscapes for both dense, old forest, and complex early-seral forest that is created by both high-severity and moderate-severity fires characteristic of historical fire regimes. Our research suggests that the latter approach may best maintain forest associated with two imperiled species that are top management concerns of federal agencies in the Sierra Nevada: the California Spotted Owl (Strix occidentalis occidentalis) and the Pacific Fisher (Pekania pennanti). We used spatially extensive US Forest Service forest survey data from 1910 and 1911, and synthesized research from other parts of this region for comparison, to assess reference conditions in low/mid-elevation Sierra Nevada forests. We found that historical ponderosa pine and mixed-conifer forests had a mixed-severity fire regime, with an average of 26% high-severity fire effects, and varied more widely in species composition and density than suggested by previous research. Our findings are contrary to other reports using a very small subset (∼6%) of the available data from these same 1910 and 1911 surveys. Therefore, we suggest that historical reference conditions of forests in the Sierra Nevada range of these species are not like that reported previously in other studies, and that mixed-severity fire, and forests defined by strong contrasts and dynamic natural processes, were characteristic of historical ponderosa pine and mixed-conifer forests of the western Sierra Nevada. Our analysis indicates that managing for both dense, old forests, and protecting complex early-seral forest created by high-severity fire, will likely advance conservation and recovery of the Spotted Owl and Pacific Fisher, while current management direction may exacerbate threats.