Analysis of ITS sequence data was used to help to elucidate species relationships in the Eupatorium mohrii complex, which includes sexual diploid and apomictic polyploids. Lack of variation and polymorphism in ITS sequences showed that E. recurvans and E. mohrii comprise diploid and autoploid populations, respectively, and should be recognized as a single species, for which the latter name has priority. Populations that collectively have been called E. anomalum, which has previously been shown to be apomictic and suggested to be of allopolyploid origin, were discovered to include two different genetic combinations that are geographically separated. The more southerly populations, including those at the type locality, were suggested by ITS sequence data to be hybrid derivatives of E. mohrii and E. rotundifolium. Northern populations from Virginia and North Carolina appeared to be hybrid derivatives of E. mohrii and E. serotinum, confirmed by data from highthroughput sequencing of the nuclear ribosomal repeat region. Because these northern populations have characteristic phenotypic features and are localized to a distinct habitat in interdune swales, they are described here as Eupatorium maritimum. A chromosome count of 2n = 30 was obtained from a sample of E. maritimum, suggesting that it is a triploid. Based on its uncommon occurrence in a habitat that is geographically restricted, E. maritimum appears to be a rare species that is in need of protection.