| Eupatorium diffusum Vahl, 1794 |
| Eupatorium dissectum (Hook. & Arn.) Benth., 1845 |
| Eupatorium divergens Less., 1830 |
| Eupatorium diversifolium Schrad., 1829 |
| Eupatorium dolichobasis McVaugh, 1972 |
| Eupatorium donnell-smithii J.M. Coult., 1891 |
| Eupatorium drepanophyllum Klatt, 1894 |
| Eupatorium dryadeum DC., 1838 |
| Eupatorium dryophilum B.L. Rob., 1901 |
| Eupatorium durangense B.L. Rob., 1907 |
| Eupatorium durangense var. angustius B.L. Rob., 1907 |
| Eupatorium eggersii Hieron., 1908 |
| Eupatorium ehrenbergii Hemsl., 1881 |
| Eupatorium enigmaticum B.L. Turner, 1989 |
| Eupatorium enixum B.L. Rob., 1923 |
| Eupatorium eriocarpum B.L. Rob. & Greenm., 1896 |
| Eupatorium erythrocomum B.L. Rob., 1907 |
| Eupatorium erythropappum B.L. Rob., 1904 |
| Eupatorium espinosarum A. Gray, 1879 |
| Eupatorium espinosarum var. ambiguum A. Gray, 1879 |