We used ITS sequences as species barcodes to evaluate 127 samples of 12 Helenium species from the eastern and central USA, focusing on a species complex of H. autumnale (76 sequences from 11 U.S. states and two Canadian provinces), the federally “threatened” H. virginicum, now recommended for delisting (30 sequences from three U.S. states), and H. flexuosum (11 sequences from four U.S. states). ITS sequences confirmed most species identifications and supported the presence of the first population of the “threatened” endemic Missouri-Virginia disjunct, Helenium virginicum, in Indiana. Because the Indiana plants grow in a restored wetland, have a cpDNA haplotype previously known only from Missouri, with a morphology similar to Missouri variants, and an herbarium search for additional populations in Indiana found none, it is unclear whether the Indiana population is natural or planted. The presence of a putative sister lineage to H. virginicum thought to exist on the Bruce Peninsula, Ontario, Canada, was not supported after sequencing 36 plants with the sister morphology that grew there along 18 km of beach fens and finding they had H. autumnale sequences. Fine-scale biogeographic patterns of intraspecific sequence variation were found mostly in H. autumnale, with centers of different base site polymorphisms found in northern North America and the Missouri Ozarks. As in a previous study, we found DNA evidence of hybridization between Helenium species in Missouri. We offer hypotheses to explain the biogeography of North American Helenium, focusing on the three species that compose the H. autumnale species complex and suggesting that H. autumnale may be a compilospecies showing incomplete lineage sorting. We encourage exploration of more Helenium species and their conspecific populations in search of fine-scale ITS base site polymorphisms to reveal emerging lineages and resolve the origins and evolutionary implications of these biogeographic patterns.