| Eupatorium skutchii B.L. Rob., 1934 |
| Eupatorium smithii B.L. Rob., 1900 |
| Eupatorium sodalis L.O. Williams, 1975 |
| Eupatorium solidaginifolium A. Gray, 1852 |
| Eupatorium solidaginoides Kunth, 1818 |
| Eupatorium solidaginoides var. typicum B.L. Rob., 1918 |
| Eupatorium sonorae A. Gray, 1853 |
| Eupatorium sordidum Less., 1831 |
| Eupatorium sorensenii (R.M. King & H. Rob.) L.O. Williams, 1975 |
| Eupatorium sphenopodum B.L. Rob., 1907 |
| Eupatorium spinaciifolium A. Gray, 1859 |
| Eupatorium spiraeifolium Sch. Bip. ex O. Hoffm., 1895 |
| Eupatorium squarrosum Cav., 1791 |
| Eupatorium stillingiaefolium DC., 1836 |
| Eupatorium stillingiifolium DC., 1836 |
| Eupatorium stipuliferum Rusby, 1895 |
| Eupatorium strictum A. Gray, 1886 |
| Eupatorium subinclusum Klatt, 1884 |
| Eupatorium subintegrum (Greene) B.L. Rob., 1925 |
| Eupatorium subpenninervium Sch. Bip. ex Klatt, 1884 |