Single nucleotide polymorphic (SNP) markers were used to characterize the genetic structure of Symphyotrichum georgianum (Alexander) G.L. Nesom, known more commonly as the Georgia aster, from 26 populations across the species' range. This species is considered vulnerable (G3) and was a candidate for listing under the Endangered Species Act. We sampled large (> 500 stems) and small (< 100 stems) populations from across the entire range for the species. Next generation sequencing was used to assess 36 SNP markers for pooled population samples, consisting of equal amounts of genomic DNA from 30 individual stems sampled across each population. Most of the genetic variation was partitioned within and less among populations, which is consistent with perennial outcrossing species. There was a significant (r = 0.506, P < 0.001) positive association between geographic distance and genetic distance among populations, indicating increasing genetic distance (genetic dissimilarity) with increasing geographic distances between populations. There was no statistically significant difference in genetic diversity between large and small populations, but trends were observed. The Georgia and North Carolina large populations were more genetically diverse than the small populations, while the small populations were more genetically diverse than the large populations in Alabama and South Carolina. Symphyotrichum georgianum is an outcrossing perennial aster with a rhizomatous growth habit. Extensive clonal growth could account for the low genetic diversity estimates from large populations; however, quantifying the extent of clonal growth within sites is beyond the scope of the current study. There was no association between genetic diversity measures and seed fill or germination rates. Additional fine scale genetic structure studies are underway to address the extent of clonal growth in these remnant populations and how that may affect viable seed production.