The perennial herb Western Jacob’s Ladder (Polemonium occidentale, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using Genotyping-by-sequencing, we examined the relationship of P. occidentale subsp. lacustre to its closest relatives, relationships among all known populations, and genetic diversity within these populations. Polemonium occidentale subsp. lacustre represents an isolated, unique lineage that diverged from its closest relatives 1.3 ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are largely genetically distinct, and show relatively little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of Polemonium occidentale subsp. lacustre may be relictual from a now-extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large population sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.