Helianthus schweinitzii (Asteraceae) is a federally endangered, endemic sunflower that only occurs in the Piedmont of North and South Carolina. This species’ habitat is relegated to disturbed sites such as roadsides, utility rights-of way, edges of woods, and other open sites. We used allozyme electrophoresis to investigate the genetic variation among 25 populations throughout the range of the species. Data collected from 11 enzyme systems representing 14 loci indicated that most populations are genetically similar and that the species, as a whole, exhibits moderate variation. Genetic distances among populations were not correlated with geographic distances. This may be due to recent fragmentation of large, contiguous populations of the sunflower into isolated groups. Conservation strategies for H. schweinitzii should include preservation and/or creation of suitable habitat and translocation of threatened populations into protected areas. Our study suggests that mitigation programs are unlikely to disturb the genetic architecture of the species or result in outbreeding depression.