Genetic diversity among and within populations of species is critical for survival in a changing world. Conservation genetics links studies of population genetic variation with conservation managers to provide scientific data for species management strategies. We study the conservation genetics of whorled sunflower, Helianthus verticillatus (Asteraceae), an endangered sunflower species endemic to the southeastern United States. Until about five years ago, only five populations were known to exist in Alabama, Georgia, and Tennessee, but additional populations of the species have been discovered in Mississippi and Virginia. Population genetic work using microsatellites revealed that the newly discovered Mississippi plants were genetically distinct from all other populations. To further investigate these new Mississippi individuals and compare them with the rest of the species, we used a combination of genome-wide SNPs and sequencing of phylogenetically informative loci to assess genetic diversity and relatedness on a small subset of individuals. We also included the closely related species, H. grosseserratus, using a collection from Shelby County, Tennessee from the University of Memphis Herbarium. This specimen was collected with only the top portion of the plant. Interestingly this sample fell within the H. verticillatus clade in some analyses. We report the comparative genetic analysis from this subset of samples and note that additional work will be required to further define the extent of genetic diversity in the whorled sunflower.