Many species are threatened with extinction and efforts are underway worldwide to restore imperiled species to their native ranges. Restoration requires knowledge of species’ historic diversity and distribution, which may not be available. For some species, many populations were extirpated and humans moved individuals beyond their native range before native diversity and distribution were documented. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native diversity and distribution by assembling a large archive of historical records documenting human-mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) coupled with a phylogenetic analysis of 19th century (before intensive fish stocking) and contemporary DNA samples. Our study of the trout in the southern Rocky Mountains uncovered six divergent lineages, two of which went extinct, probably in the early 20th century. A third lineage, previously declared extinct, was discovered surviving in a single stream outside of its native range. Comparison of the historic and modern distributions with stocking records revealed that the current distribution of trout largely reflects intensive stocking early in the late 19th and early 20th century from two phylogenetically and geographically distinct sources. Our documentation of recent extinctions, undescribed lineages, errors in taxonomy, and dramatic range changes induced by human movement of fish underscores the importance of the historical record when developing and implementing conservation plans for threatened and endangered species.