One longstanding taxonomic question in the genus Magnolia is whether Magnolia pyramidata (=Magnolia fraseri ssp. pyramidata) is truly a subspecies of Magnolia fraseri or whether these represent two independently evolving lineages. This question presents real challenges for conservation collections and in situ conservation management (e.g. assisted migration, genetic rescue). Magnolia pyramidata individuals are currently threatened (IUCN Red List Endangered) by habitat loss and climate change. Whereas M. fraseri inhabits more mountainous regions in the United States, M. pyramidata is found within the coastal plain, with a concentrated distribution in southern Alabama and the Florida Panhandle. We are assessing population genetic diversity and structure and the species status of M. pyramidata using high throughput sequencing. We have sampled individuals from the wild as well as botanic gardens and herbaria. We are utilizing the Angiosperms353 bait set in addition to the Magnoliaceae specific bait set. We will present results of population genetic and phylogenomic analyses.