Molecular phylogenetic studies were conducted to clarify the phylogenetic placement of Conoclinium within Eupatorieae and to analyze interspecific relationships in the genus. Analysis of a six gene data set placed Conoclinium sister to Ageratum and closely related to Fleischmannia and Paneroa, a result that is consistent with the overall appearance and the phytochemistry of these genera but not with their current subtribal placement. Results of an analysis of noncoding DNA, including the chloroplast trnH-psbA spacer and the nuclear ITS and ETS regions, was consistent with the close relationship of Conoclinium to Ageratum, Fleischmannia, and Paneroa, and showed Conoclinium to be monophyletic. Within Conoclinium, the results of the phylogenetic analyses were slightly at variance with current classification, and it is suggested that C. dichotomum (populations from peninsular Florida previously included within C. coelestinum) and C. oligolepis (formerly C. betonicifolium var. integrifolium) be recognized as distinct species. The low overall sequence variability suggests that Conoclinium is a relatively recent arrival in eastern North America. Conoclinium mayfieldii is not monophyletic and the Sierra Madre Occidental populations of the species are herein recognized as a new species, C. gonzaleziae. Neotypes for C. dichotomum and C. oligolepis are designated.